Reversible modification of nucleotides

ABSTRACT

Disclosed herein, inter alia, are methods for modifying a nucleotide, for example including reacting a nucleotide having a 3′-O-oxime moiety such as 
     
       
         
         
             
             
         
       
     
     with a reagent having an —ONH 2  moiety to produce a nucleotide having a 3′-O—NH 2  moiety such as 
     
       
         
         
             
             
         
       
     
     wherein the reagent having the —ONH 2  moiety further comprises alkyl, alkenyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl, or (heteroalicyclyl)alkyl.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.17/016,992, filed Sep. 10, 2020, which claims the benefit of U.S.Provisional Application No. 62/898,152, filed Sep. 10, 2019, which areincorporated herein by reference in their entireties and for allpurposes.

BACKGROUND

The present disclosure relates generally to reversible blocking ofnucleotides and nucleic acids to inhibit enzyme catalyzed modificationof their 3′ hydroxyl moieties, and has specific applicability to nucleicacid sequencing processes that employ cyclic reversible termination.

Genomes have been analogized as operating manuals containinginstructions for development and functioning of individual organisms.Genomes have been shown to guide growth and development, direct thefunction of vital organs, influence mood and behavior, etc. Theuniqueness of every individual is derived in significant part from theunique composition of their genome. The differences between individualscan be observed as differences in the sequence of nucleotides in the DNAthat constitutes their genome. Great strides have been made inidentifying how those sequence differences predict risk of disease,chances of having adverse reactions to certain therapeutic drugs, andchances of having certain abilities and personality traits, to name afew.

Recently, the diagnostic potential for genomic information hasaccelerated due to commercialization of DNA sequencing platforms thatare capable of sequencing at the scale of the typical human genome,which has a sequence of 3 billion nucleotides. Although the throughputand cost for sequencing have improved vastly over the last few decades,there are still many diseases for which diagnostic sequence signatureshave not been identified and the cost of sequencing is still out ofreach for many clinical applications.

Many sequencing technologies that have been developed, including severalthat are in wide commercial use, employ a cyclic reversible terminator(CRT) process. The CRT process extends a primer along a DNA template ofinterest such that each cycle results in detection of a single positionin the template. The cycles are repeated to effectively walk down thetemplate in DNA while reading the sequence in single nucleotide steps.Performing 100 CRT cycles produces a sequence read of 100 nucleotides.Single nucleotide step size, and as a result single nucleotideresolution for the resulting sequence read, is achieved by incrementingthe primer with a nucleotide having a 3′ reversible terminator moiety.The primer, after adding the reversibly terminated nucleotide, cannot befurther extended until it is treated with an appropriate deblockingreagent to remove the reversible terminator moiety. The accuracy andread length of most CRT processes, including those that are incommercial use today, are known to be compromised due to inefficienciesin the steps that incorporate reversible terminators into primers and inthe steps used for deblocking the primers. Moreover, many CRT processesuse deblocking reagents that can damage the very DNA that is to besequenced. Because sequencing is a cumulative process, even smallinefficiencies in primer extension, primer deblocking and resistance toDNA damage can add up to a substantial adverse impact over the manycycles of a sequencing process.

Thus, there exists a need for improved reagents and methods forreversible termination of nucleotides and nucleic acids. The presentinvention satisfies this need and provides related advantages as well.

BRIEF SUMMARY

The present disclosure provides a composition that includes solutioncontaining a nucleotide having a protecting group such as a 3′-O-oximemoiety and a reagent to remove the protecting group and deliver to theprotecting group's position a blocking group, such as a reagent havingthe structure R2-ONH₂. A number of R2 moieties are consistent with thepresent disclosure. In some cases, R2 is independently alkyl, alkenyl,alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof. Alternately or in combination,R2 comprises a moiety having a molecular weight of at least 24, at least25, at least 26, at least 27, at least 28, at least 29, at least 30, atleast 31, at least 32, at least 33, at least 34, at least 35, at least36, or greater than 36 g/mol. Similarly, an R2 moiety as contemplatedherein has a molecular weight of no more than 1000, no more than 500, nomore than 400, no more than 300, no more than 250, no more than 200, nomore than 150, or no more than 100 g/mol. Alternately or in combination,various R2 embodiments comprise one or more of the following: at leasttwo carbon nuclei, fluorine nucleus, a phosphorous nucleus, a nitrogennucleus, a silicon nucleus, an oxygen nucleus, a hydroxy moiety,heterocyclic ring, a phenyl ring, or other moiety, alone or incombination with one another.

In particular configurations, a representative nucleotide startingmaterial for methods or compositions herein has the structure:

B can be a nucleobase. R1 can independently be a halogen, OCH₃, H or OH,or may carry an alternate modification at the 2′ R1 position, such thatthe nucleotide is variously a ribonucleotide or a deoxyribonucleotide. Qcan be independently monophosphate, diphosphate, triphosphate, nucleicacid, hydrogen, or other moiety, such as a surface or linker bonded to asurface. R3 and R4 can be independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof. By way of example, theprotecting group moiety at the 3′ position of the nucleotide can be analdoxime (such that one of R3 or R4 is hydrogen) or a ketoxime (whereinneither R3 nor R4 is hydrogen). Other protecting group moieties arecontemplated herein and consistent with the present disclosure.

The present disclosure also provides methods for modifying a nucleotide.The methods can be carried out by reacting a nucleotide having aprotecting group such as a 3′-O-oxime moiety with a reagent to removethe protecting group and deliver to the protecting group's position ablocking group, such as a reagent having the structure R2-ONH₂ toproduce a nucleotide having a 3′-O—NH₂ moiety, wherein R2 isindependently R2 is —C(R6)(R7)(R8), —C(O)(R6), —P(O)(R6)(R7),—C(R6)(═C(R7)(R8)), —Si(R6)(R7)(R8), —S O₂(R6), substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C5-C6), substituted orunsubstituted cycloalkenyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆), substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆),substituted or unsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3to 6 membered, or 5 to 6 membered), substituted or unsubstituted aryl(e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl), or substituted orunsubstituted heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9membered heteroaryl, or 5 to 6 membered heteroaryl). In some cases R2 isindependently alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl,cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl,(heteroalicyclyl)alkyl, or an optionally substituted variant thereof. R2moieties may comprise a number of constituents, alone or in combination,to covey the benefits disclosed herein. Some R2 moieties variouslycomprise at least 2, at least 3, at least 4, at least 5, at least 6, ormore than 6 carbon nuclei. Similarly, some R2 comprise at least one ofthe following: at least 1 nitrogen nucleus, at least one siliconnucleus, at least one phosphorous nucleus, at least one fluorine nucleusor at least one other constituent. R2 moieties are in some casespartially or fully fluorinated, or partially or fully hydrogenated. Insome cases an R2 moiety comprises at least one component to facilitatesolubility. Reagents having structures to deliver alternate blockinggroups or reversible terminator moieties, such as ONHCH₃, O—CH₂N₃, orother moiety such as those consistent with reversible termination ofnucleic acid extension, are also contemplated herein. In someconfigurations, the nucleotide that has the 3′-O-oxime moiety can havethe structure:

and the nucleotide that has the 3′-O—NH₂ moiety can have the structure:

B can be a nucleobase. R1 can independently be a halogen, OCH₃, H or OH.Q can be independently monophosphate, diphosphate, triphosphate, nucleicacid, or other moiety, such as a surface or linker bonded to a surface.R3 and R4 can be independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof. By way of example, the moiety atthe 3′ position of the nucleotide can be an aldoxime (such that one ofR3 or R4 is hydrogen) or a ketoxime (neither of R3 or R4 is hydrogen).In particular configurations, a nucleotide starting material for methodsor compositions herein has the structure:

B can be a nucleobase. R1 can independently be a halogen, OCH₃, H or OH.Q can be independently monophosphate, diphosphate, triphosphate, nucleicacid, or other moiety, such as a surface or linker bonded to a surface.R3 and R4 can be independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof. By way of example, theprotecting group moiety at the 3′ position of the nucleotide can be analdoxime (such that one of R3 or R4 is hydrogen) or a ketoxime (whereinneither R3 nor R4 is hydrogen). Other protecting group moieties arecontemplated herein and consistent with the present disclosure. Thepresent disclosure also provides methods for modifying a nucleotide. Themethods can be carried out by reacting a nucleotide having a protectinggroup such as a 3′-O-oxime moiety with a reagent to deliver a blockinggroup, such as a reagent having the structure R2-ONH₂ to produce anucleotide having a 3′-O—NH₂ moiety, wherein R2 is independently alkyl,alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl,heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl,(heteroalicyclyl)alkyl, or an optionally substituted variant thereof.Reagents having structures to deliver alternate blocking groups, such asONHCH₃, O—CH₂N₃, or other moiety consistent with reversible terminationof nucleic acid extension, are also contemplated herein.

The present disclosure further provides a kit that includes a firstvessel containing a nucleotide having a 3′-O-oxime moiety and a secondvessel containing a reagent having the structure R2-ONH₂, wherein R2 isindependently alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl,cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl,(heteroalicyclyl)alkyl, or an optionally substituted variant thereof. Insome configurations, the nucleotide can have the structure:

B can be a nucleobase. R1 can independently be a halogen, OCH₃, H or OH.Q can be independently monophosphate, diphosphate, triphosphate, nucleicacid, or other moiety, such as a surface or linker bonded to a surface.R3 and R4 can be independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof. By way of example, the moiety atthe 3′ position of the nucleotide can be an aldoxime (such that one ofR3 or R4 is hydrogen) or a ketoxime (neither of R3 or R4 is hydrogen).

BRIEF DESCRIPTION OF THE DRAWING

FIG. 1A shows a plot of percent nucleotide degradation vs. percentconsumption of the 3′-O—(N-acetone oxime) moiety for 3′-O—(N-acetoneoxime)-dCTP when treated with various candidate DRT (‘deblockingreversible terminator’) aminooxy reagents sharing an —O—NH₂ reversibleterminator moiety tethered to various R2 groups. Reactions wereperformed as described in Example 1 and assayed after 1 hour for a 25 Creaction. FIG. 1A illustrates that as R2 increases in molecular weight,one sees a decrease in dC degradation. Similarly, as R2 increases inmolecular weight, one sees an increase in starting material consumption.FIG. 1B lists the chemical identities of the DRT reagents assayed inFIG. 1A, indicating their various R2 moieties.

FIG. 2 presents examples of deblocking reagents. All examples in thisfigure share a common —O— NH₂ reversible terminator moiety (at right ineach molecule as presented) tethered to various R2 groups (at left ineach molecule as presented) ranging in molecular weight and chemicalstructure. Similar deblocking reagents having R2 groups as disclosedherein tethered to alternate reversible terminator moieties, such as—O—NHCH₃, —O—CH₂N₃, or other moiety such as those consistent withreversible termination of nucleic acid extension, are also contemplatedherein in combination with the R2 moieties presented here or otherwisedisclosed herein.

FIG. 3. Example of a deblocking side reaction with cytidine. This sidereaction accounts for at least some of the dC degradation quantified inFIG. 1A. As indicated in FIG. 1A, with increasing R2 size one sees andecrease in the side reaction depicted herein.

DETAILED DESCRIPTION

The present disclosure provides compositions and methods that are usefulfor synthesis of nucleotides having moieties at the 3′ position, such asmoieties that protect the 3′ position from modifications such aschemical modifications and enzymatic modifications, such as addition ofa nucleotide as effected by template directed DNA polymerase enzymes. Anucleotide that is protected in this way can be referred to as beingblocked or terminated. For example, when a nucleotide having a protected3′ position is incorporated into an extending nucleic acid strand as the3′ nucleotide moiety of a nucleic acid primer, the extended primer iseffectively blocked from being further extended by a polymerase orligase. In other words, primer extension has been terminated.

In particular configurations or embodiments, a blocked or terminatednucleotide can have a reversible terminator moiety such as a 3′-ONH₂moiety that, unlike the native hydroxyl found at the 3′ position ofdeoxyribonucleotides and ribonucleotides, is resistant to modificationby certain enzymes and chemical reagents. Under certain conditions the3′-ONH₂ moiety can be chemically converted to a hydroxyl, for examplewhen the blocked nucleotide is treated with an acid such as nitrousacid. Replacement of the —O—NH₂ moiety as a whole with an —OH moiety orreplacement of the —NH₂ moiety with an —H both effectively result indeblocking, and the fate of the 3′ O in deblocking is immaterial, solong as the final product has a 3′ OH available for polymerase-mediatednucleic acid extension. As such the 3′-ONH₂ moiety functions as areversible terminator when coupled with the deblocking reagents of thepresent disclosure. Other reversible terminators that are readilyremoved to recover a 3′ hydroxy moiety compatible with enzymatic strandextension are consistent with the disclosure herein, such that not allembodiments herein are limited to the preparation of a nucleotide havinga 3′-O—NH₂ moiety. Exemplary alternatives include include 3′-O—NHCH₃,—O—CH₂N₃, and others known in the art that block strand extension whenattached at the 3′ position of the 3′ end of a nucleic acid strand,while at the same time do not preclude binding by a DNA or other nucleicacid polymerase such that nucleotides carrying such reversibleterminators may be added, at their 5′ ends, to the 3′ hydroxy groups ofunblocked nucleotides or nucleotide polymers to produce 3′ terminatednucleic acid strands.

Reversible termination of nucleotides are useful for a variety ofapplications. For example, a variety of nucleic acid sequencingplatforms utilize a cyclic reversible terminator (CRT) process in whichthe sequence of a template nucleic acid is read while incrementallyextending a primer nucleic acid along the template. Incrementalextension can be achieved in CRT processes by structuring each cycle toinclude a step of extending the primer through addition of a reversiblyterminated nucleotide (or oligonucleotide reversibly terminated at its3′ end) followed by deblocking the extended primer. In each cycle, adetection step is also carried out in order to identify the type ofnucleotide that is present at a particular position that has beenaligned with respect to the extended primer.

The reversibly terminated nucleotides, and methods for their synthesis,set forth herein provide advantages of very efficiently replacing 3′protecting groups such as 3′-O-oximes or other groups added tofacilitate the chemical manipulation of other regions of a nucleic acid,such as addition of a triphosphate moiety to a nucleotide 5′ position.Without being bound by theory, it is predicted that because CRT is agenerally cumulative process, any errors or inefficiencies in blockingand deblocking steps will produce a cumulatively adverse effect. Forexample, phasing is the phenomenon whereby individual nucleic acidmolecules within a population lose sync with each other during thecourse of a CRT process, for example due to a defect in removal of ablocking group, leading to failure to incorporate an additional moietyduring one or more cycles of a CRT process. Phasing can manifest asextension of one or more primer molecules ‘falling behind’ the others inthe population, or alternately as a defect leading to one or more primermolecules ‘going ahead’ of others in the population. A phasing rate of,for example, only 0.5% per cycle may result in an accumulated loss ofroughly half of true signal for a sequencing or other CRT reaction after120 cycles. The problem is exacerbated by the proportional increase inbackground noise due to false signals that arise from members of thepopulation that are out of phase. The accumulated loss insignal-to-noise results in a limitation on read length (which, in turn,results in reduced sequencing throughput) and increased errorsespecially for later cycles as noise overwhelms signal. The reversiblyterminated nucleotides set forth herein can be used to inhibitdisruptions in extension phase, thereby improving accuracy and readlength reactions such as in nucleic acid sequencing processes. Throughpractice of the methods and use of the compositions disclosed herein,nucleotide compositions are generated having a very high degree ofreplacement of a protecting group such as —O-oxime by a reversible groupsuch as an —O—NH₂, with a low rate of dC degradation, as depicted inFIG. 1A and as is applicable generally to the R2 moieties disclosedherein. Consequently, reagents generated using the compositions hereinor through the methods disclosed herein are in some cases suitable foraddition into a nucleic acid sequencing reagent, such as direct additionwithout further clean-up or purification, to produce a sequencingreaction run having a high degree of accuracy over a substantial lengthof a run, as depicted in Example 2, below. Such a reagent may furthercomprise a polymerase surfactant, buffer or other reagent suitable fordirect addition into a sequencing device. Without being bound to theory,the performance of a run such as that presenteded in Example 2 is atleast in part due to decreases in phasing defects which may otherwiseresult from inefficient replacement of a protecting group such as an—O-oxime group with a reversible terminator such as —O—NH₂, resulting ineither retained protecting groups, unblocked 3′ OH moieties, or degradeddC bases along the lines of those presented in FIG. 3.

Without being bound by theory, one possible advantage of the syntheticmethods and compositions set forth herein for blocking the 3′ positionof a nucleotide is that the methods are relatively inert to unwantedside reactions with other moieties of the nucleotide. Accordingly,reversibly terminated nucleotides that are made by methods or involvingthe compositions set forth herein may not be substantially destroyed ormodified in ways that carry over into adverse effects during blockingand deblocking steps that occur during a CRT process or otherbiochemical process that utilizes the reversibly terminated nucleotides.In various cases, no more than 6%, no more than 5%, no more than 4%, nomore than 3%, no more than 2%, no more than 1% or less than 1% of thenucleotides, such as cytosine nucleotides, used in a reaction orrepresented in a composition herein are modified or degraded through thepractice of the disclosure. Accordingly, the methods and compositionsset forth herein provide improved sequencing accuracy by providing asequencing starting material that is relatively free of degraded ormodified bases such as degraded or modified cytosine that may interferewith the accuracy, phase or read length of a sequencing reaction.Similarly, the methods and compositions set forth herein facilitate theproduction of nucleic acid sequencing reagents by generating reversiblyterminated nucleotides of a purity that can be, in some cases, directlyadded to a sequencing reagent without further purification or isolation.

Accordingly, compositions as disclosed herein or produced throughmethods disclosed herein facilitate accurate sequencing by being or bygenerating reversibly terminated nucleotides that are relatively clearof degraded or modified bases such as degraded or modified cytosinebases, while being relatively clear of retained 3′ protecting groupssuch as —O-oximes, and having a relatively low concentration ofunblocked 3′ OH groups. These features, alone or in combination,facilitate sequencing accuracy, phasing or read length of a sequencingreaction. In addition, the higher efficiency of methods and purity ofcompositions resulting from these methods facilitates morecost-effective sequencing because the compositions require lesspurification prior to their employment in sequencing reactions, and arein some cases added directly into a sequencing reagent or kit withoutfurther isolation or purification.

Definitions

Terms used herein will be understood to take on their ordinary meaningin the relevant art unless specified otherwise. Several terms usedherein and their meanings are set forth below.

Where substituent groups are specified by their conventional chemicalformulae, written from left to right, they equally encompass thechemically identical substituents that would result from writing thestructure from right to left, e.g., —CH₂O— is equivalent to —OCH₂—.Where a substituent group or moiety is written with internal bondsdepicted, it will be understood that the substituent group or moiety mayalso be depicted without internal bonds explicitly drawn and bothrepresentation will be understood to be the same substituent group ormoiety, for example —ONH₂ and —O—NH₂ are the same group.

As used herein, “alkenyl” refers to an alkyl that contains in thestraight or branched hydrocarbon chain one or more double bonds. Analkenyl moiety may be unsubstituted or substituted. An alkenyl moietycan, optionally, have a number of carbon atoms that is in a rangeexemplified herein for alkyl moieties.

As used herein, “alkoxy” refers to the formula —OR wherein R is analkyl, an alkenyl, an alkynyl, a cycloalkyl, a cycloalkenyl or acycloalkynyl. A non-limiting list of alkoxys is methoxy, ethoxy,n-propoxy, 1-methylethoxy (isopropoxy), n-butoxy, iso-butoxy,sec-butoxy, or tert-butoxy. An alkoxy moiety may be substituted orunsubstituted.

As used herein, “alkoxyamine” refers to the formula R′—ONR₂ wherein R′is an alkyl, an alkenyl, an alkynyl, a cycloalkyl, a cycloalkenyl or acycloalkynyl. A non-limiting list of alkoxys is methoxy, ethoxy,n-propoxy, 1-methylethoxy (isopropoxy), n-butoxy, iso-butoxy,sec-butoxy, or tert-butoxy, wherein R′ is not hydrogen, and wherein oneor both R groups that are bonded to nitrogen is independently ahydrogen, an alkyl, an alkenyl, an alkynyl, a cycloalkyl, a cycloalkenylor a cycloalkynyl. A non-limiting list of alkoxys is methoxy, ethoxy,n-propoxy, 1-methylethoxy (isopropoxy), n-butoxy, iso-butoxy,sec-butoxy, or tert-butoxy. An alkoxyamine moiety may be substituted orunsubstituted.

As used herein, “alkyl” refers to a straight or branched hydrocarbonchain that comprises a fully saturated (no double or triple bonds)hydrocarbon moiety. Alkyl is an uncyclized chain. In some embodiments,the alkyl moiety may have 1 to 20 carbon atoms (whenever it appearsherein, a numerical range such as “1 to 20” refers to each integer inthe given range inclusive of the endpoints; e.g., “1 to 20 carbon atoms”means that the alkyl moiety may consist of 1 carbon atom, 2 carbonatoms, 3 carbon atoms, etc., up to and including 20 carbon atoms,although the present definition also covers the occurrence of the term“alkyl” where no numerical range is designated). The alkyl moiety mayalso be a medium size alkyl having about 7 to about 10 carbon atoms. Thealkyl moiety can also be a lower alkyl having 1 to 6 carbon atoms. Thealkyl moiety of the compounds may be designated as “C₁-C₄ alkyl” orsimilar designations. By way of example only, “C₁-C₄ alkyl” indicatesthat there are one to four carbon atoms in the alkyl chain, i.e., thealkyl chain is selected from methyl, ethyl, propyl, iso-propyl, n-butyl,iso-butyl, sec-butyl, and t-butyl. Typical alkyl moieties include, butare in no way limited to, methyl, ethyl, propyl, isopropyl, butyl,isobutyl, tertiary butyl, pentyl, and hexyls. The alkyl moiety may besubstituted or unsubstituted. An alkyl moiety having at least two carbonatoms can be particularly useful, for example, when a methyl moiety isless effective than a longer chain alkyl moiety.

As used herein, “alkynyl” refers to an alkyl that contains in thestraight or branched hydrocarbon chain one or more triple bonds. Analkynyl moiety may be unsubstituted or substituted. An alkynyl moietycan, optionally, have a number of carbon atoms that is in a rangeexemplified herein for alkyl moieties.

The term “alkylene,” by itself or as part of another substituent, means,unless otherwise stated, a divalent radical derived from an alkyl, asexemplified, but not limited by, —CH₂CH₂CH₂CH₂—. Typically, an alkyl (oralkylene) group will have from 1 to 24 carbon atoms, with those groupshaving 10 or fewer carbon atoms being preferred herein. A “lower alkyl”or “lower alkylene” is a shorter chain alkyl or alkylene group,generally having eight or fewer carbon atoms. The term “alkenylene,” byitself or as part of another substituent, means, unless otherwisestated, a divalent radical derived from an alkene. The term “alkynylene”by itself or as part of another substituent, means, unless otherwisestated, a divalent radical derived from an alkyne.

The term “heteroalkyl,” by itself or in combination with another term,means, unless otherwise stated, a stable straight or branched chain, orcombinations thereof, including at least one carbon atom and at leastone heteroatom (e.g., O, N, P, Si, and S), and wherein the nitrogen andsulfur atoms may optionally be oxidized, and the nitrogen heteroatom mayoptionally be quaternized. The heteroatom(s) (e.g., O, N, S, Si, or P)may be placed at any interior position of the heteroalkyl group or atthe position at which the alkyl group is attached to the remainder ofthe molecule. Heteroalkyl is an uncyclized chain. Examples include, butare not limited to: —CH₂—CH₂—O—CH₃, —CH₂—CH₂—NH—CH₃,—CH₂—CH₂—N(CH₃)—CH₃, —CH₂—S—CH₂—CH₃, —CH₂—S—CH₂, —S(O)—CH₃,—CH₂—CH₂—S(O)₂—CH₃, —CH═CHO—CH₃, —Si(CH₃)₃, —CH₂—CH═N—OCH₃,—CH═CH—N(CH₃)—CH₃, —O—CH₃, —O—CH₂—CH₃, and —CN. Up to two or threeheteroatoms may be consecutive, such as, for example, —CH₂—NH—OCH₃ and—CH₂—O—Si(CH₃)₃. A heteroalkyl moiety may include one heteroatom (e.g.,O, N, S, Si, or P). A heteroalkyl moiety may include two optionallydifferent heteroatoms (e.g., O, N, S, Si, or P). A heteroalkyl moietymay include three optionally different heteroatoms (e.g., O, N, S, Si,or P). A heteroalkyl moiety may include four optionally differentheteroatoms (e.g., O, N, S, Si, or P). A heteroalkyl moiety may includefive optionally different heteroatoms (e.g., O, N, S, Si, or P). Aheteroalkyl moiety may include up to 8 optionally different heteroatoms(e.g., O, N, S, Si, or P). The term “heteroalkenyl,” by itself or incombination with another term, means, unless otherwise stated, aheteroalkyl including at least one double bond. A heteroalkenyl mayoptionally include more than one double bond and/or one or more triplebonds in additional to the one or more double bonds. The term“heteroalkynyl,” by itself or in combination with another term, means,unless otherwise stated, a heteroalkyl including at least one triplebond. A heteroalkynyl may optionally include more than one triple bondand/or one or more double bonds in additional to the one or more triplebonds. In embodiments, the carbon-carbon bonds of a heteroalkyl may befully saturated (no double or triple carbon-carbon bonds).

Similarly, the term “heteroalkylene,” by itself or as part of anothersubstituent, means, unless otherwise stated, a divalent radical derivedfrom heteroalkyl, as exemplified, but not limited by,—CH₂—CH₂—S—CH₂—CH₂— and —CH₂—S—CH₂—CH₂—NH—CH₂—. For heteroalkylenegroups, heteroatoms can also occupy either or both of the chain termini(e.g., alkyleneoxy, alkylenedioxy, alkyleneamino, alkylenediamino, andthe like). Still further, for alkylene and heteroalkylene linkinggroups, no orientation of the linking group is implied by the directionin which the formula of the linking group is written. For example, theformula —C(O)₂R′— represents both —C(O)₂R′— and —R′C(O)₂—. As describedabove, heteroalkyl groups, as used herein, include those groups that areattached to the remainder of the molecule through a heteroatom, such as—C(O)R′, —C(O)NR′, —NR′R″, —OR′, —SR′, and/or —SO₂R′. Where“heteroalkyl” is recited, followed by recitations of specificheteroalkyl groups, such as —NR′R″ or the like, it will be understoodthat the terms heteroalkyl and —NR′R″ are not redundant or mutuallyexclusive. Rather, the specific heteroalkyl groups are recited to addclarity. Thus, the term “heteroalkyl” should not be interpreted hereinas excluding specific heteroalkyl groups, such as —NR′R″ or the like.The term “heteroalkenylene,” by itself or as part of anothersubstituent, means, unless otherwise stated, a divalent radical derivedfrom a heteroalkene. The term “heteroalkynylene” by itself or as part ofanother substituent, means, unless otherwise stated, a divalent radicalderived from a heteroalkyne.

As used herein, “amine” refers to a —NR₂ moiety wherein one or more Rgroup can be independently hydrogen, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, or (heteroalicyclyl)alkyl. In embodiments,each R group is independently substituted or unsubstituted.

As used herein, “aminooxy” refers to —O—NR₂ moiety, wherein one or moreR group can be independently hydrogen, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, or (heteroalicyclyl)alkyl. In embodiments,each R group is independently substituted or unsubstituted.

As used herein, “array” refers to a population of molecules attached toone or more solid support such that the molecules at one site can bedistinguished from molecules at other sites. An array can includedifferent molecules that are each located at different addressable siteson a solid support. Alternatively, an array can include separate solidsupports each functioning as a site that bears a different molecule,wherein the different molecules can be identified according to thelocations of the solid supports on a surface to which the solid supportsare attached, or according to the locations of the solid supports in aliquid such as a fluid stream. The molecules of the array can be, forexample, nucleotides, nucleic acids, nucleic acid primers, nucleic acidtemplates, primed template nucleic acids, or nucleic acid enzymes suchas polymerases, ligases, exonucleases or combinations thereof.

As used herein, “aryl” refers to a carbocyclic (all carbon) monocyclicor multicyclic aromatic ring system (including, e.g., fused, bridged, orspiro ring systems where two carbocyclic rings share a chemical bond,e.g., one or more aryl rings with one or more aryl or non-aryl rings)that has a fully delocalized pi-electron system throughout at least oneof the rings. The number of carbon atoms in an aryl moiety can vary. Forexample, in some embodiments, the aryl moiety can be a C₆-C₁₄ arylmoiety, a C₆-C₁₀ aryl moiety, or a C₆ moiety. Examples of aryl moietiesinclude, but are not limited to, benzene, naphthalene, and azulene. Anaryl moiety may be substituted or unsubstituted. In various embodiments,an aryl moiety is independently a phenyl or naphthyl. In embodiments, afused ring aryl refers to multiple rings fused together wherein at leastone of the fused rings is an aryl ring and wherein the multiple ringsare attached to the parent molecular moiety through any carbon atomcontained within an aryl ring of the multiple rings. An “arylene”, aloneor as part of another substituent, means a divalent radical derived froman aryl.

As used herein, “aralkyl” and “aryl(alkyl)” refer to an aryl connected,as a substituent, via a lower alkylene moiety. The lower alkylene andaryl moiety of an aralkyl may be substituted or unsubstituted. Examplesinclude but are not limited to benzyl, 2-phenylalkyl, 3-phenylalkyl, andnaphthylalkyl.

As used herein, “attached” refers to the state of two things beingjoined, fastened, adhered, connected or bound to each other. Forexample, a nucleic acid can be attached to a solid phase support by acovalent or non-covalent bond. Similarly, two nucleic acids can beattached to each other by a covalent (e.g. phosphodiester) bond or by anon-covalent bond (e.g. hydrogen bonding between bases of the twonucleic acids). A covalent bond is characterized by the sharing of pairsof electrons between atoms. A non-covalent bond is a chemical bond thatdoes not involve the sharing of pairs of electrons and can include, forexample, hydrogen bonds, ionic bonds, van der Waals forces, hydrophilicinteractions and hydrophobic interactions.

As used herein, “blocking moiety,” when used in reference to anucleotide, means a part of the nucleotide that inhibits or prevents the3′ oxygen of the nucleotide from forming a covalent linkage to anothernucleotide or to an oligonucleotide. For example, a blocking moiety caninhibit or prevent polymerase catalyzed formation of a covalent linkagebetween the 3′ position of the nucleotide and a next correct nucleotideduring a nucleic acid polymerization reaction. Similarly, a blockingmoiety can inhibit or prevent ligase catalyzed formation of a covalentlinkage between the 3′ position of the nucleotide and an oligonucleotideduring a nucleic acid ligation reaction. Notably, blocking moieties ascontemplated herein do not interfere with incorporation of the blockedbase into an extending primer strand (e.g., catalyzed by a polymerase);rather, once incorporated, a blocked nucleotide interferes withsubsequent elongation because the 3′ end of the nucleotide isinaccessible to the 5′ phosphate of a subsequent nucleotide. Theblocking moiety of a “reversibly terminated” nucleotide can be removedfrom the nucleotide analog, or otherwise modified, without substantialharm to the extending primer strand or its complement, to allow the3′-oxygen of the nucleotide to be available to covalently link toanother nucleotide or to an oligonucleotide. Such a blocking moiety maybe referred to herein as a “reversible terminator moiety” because theblocking of primer extension is reversed through removal of the blockingor terminator moiety. A nucleotide that has a blocking moiety such as areversible terminator moiety can be at the 3′ end of a nucleic acid,such as a primer, or can be a monomeric molecule that is not covalentlyattached to a nucleic acid. Exemplary blocking moieties include 3′ ONH₂,as well as 3′ ONHCH₃ and 3′ O methylazide (3′-OCH₂N₃). In variousembodiments, a protecting moiety may also be a blocking moiety (e.g., a3′-O-oxime moiety may be a blocking moiety). As used herein, R2-block isR2 bonded to a blocking moiety such as a reversible terminator moiety.R2-moieties in solution are in some cases used to stabilize blockingmoieties so as to prevent their unwanted removal from nucleotides toform 3′ OH groups compatible with polymerase-mediated extension.

As used herein, a “protecting moiety” is a moiety that protects amolecule to which it is attached from cross-reaction or misdirectedreaction during a chemical process, such as a nonenzymatic process or anonspecific chemical process. Unlike blocking moieties such asreversible terminating moieties, protecting moieties are not necessarilyreadily removed without risk of cross-reaction or degradation to theprotected molecule. Exemplary moieties include 3′-O-oxime moieties suchas 3′-O-alkoximes or 3′ O-ketoximes, which protect ribose 3′ positionsfrom cross reaction during 5′ phosphorylation reactions, for example. Invarious embodiments, a protecting moiety is a 3′-O-oxime (e.g.,3′-O-alkoxime or 3′-O-ketoxime). In embodiments, the protecting moietyprevents reactivity of the 3′ carbon or 3′ oxygen of a nucleotide ornucleoside during a phosphorylation reaction of the nucleotide ornucleoside, such as may occur during the addition of a triphosphatemoiety to a nucleotide 5′ position.

The term “comprising” is intended herein to be open-ended, includingrecited elements, but also leaving open the possibility of includingadditional, unrecited elements.

As used herein, “cycloalkyl” refers to a completely saturated (no doubleor triple bonds) mono- or multi-cyclic hydrocarbon ring system. Whencomposed of two or more rings, the rings may be joined together in afused fashion. A cycloalkyl moiety can contain 3 to 10 atoms in thering(s). In some molecules, a cycloalkyl moiety can contain 3 to 8 atomsin the ring(s). A cycloalkyl moiety may be unsubstituted or substituted.Typical cycloalkyl moieties include, but are not limited to,cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl, andcyclooctyl.

As used herein, “cycloalkenyl” refers to a mono- or multi-cyclichydrocarbon ring system that contains one or more double bonds in atleast one ring; although, if there is more than one, the double bonds donot form a fully delocalized pi-electron system throughout all the rings(otherwise the moiety would be “aryl,” as defined herein). When composedof two or more rings, the rings may be connected together in a fusedfashion. A cycloalkenyl moiety may be unsubstituted or substituted. A“cycloalkylene”, alone or as part of another substituent, means adivalent radical derived from a cycloalkyl.

As used herein, “cycloalkynyl” refers to a mono- or multi-cyclichydrocarbon ring system that contains one or more triple bonds in atleast one ring. If there is more than one triple bond, the triple bondsdo not form a fully delocalized pi-electron system throughout all therings. When composed of two or more rings, the rings may be joinedtogether in a fused fashion. A cycloalkynyl moiety may be unsubstitutedor substituted.

As used herein, “deblock” means to remove or modify a blocking moietysuch as a reversible terminator moiety of a nucleotide to render thenucleotide extendable, such as through exposure of or generation of a 3′OH. Such a deblocked nucleotide or nucleic acid strand is capable offorming a phosphodiester bond with a second nucleotide, rendering thenucleotide capable of forming a phosphodiester bond involving the 3′carbon of the nucleotide and the 5′ carbon of a second nucleotide). Forexample, a reversibly terminated nucleotide can be present at the 3′ endof a primer such that deblocking renders the primer extendable.Alternatively, the nucleotide can be in monomeric form when deblocked.

As used herein, the term “each,” when used in reference to a collectionof items, is intended to identify an individual item in the collectionbut does not necessarily refer to every item in the collection.Exceptions can occur if explicit disclosure or context clearly dictatesotherwise.

As used herein, the phrase “at least one element selected from the listof” A, B, and C is intended to read on sets including one element fromthe list, two elements form the list or all elements of the list, andmay but is not necessarily intended to require a representative of eachelement A, B, and C unless otherwise designated.

As used herein, “exogenous,” when used in reference to a moiety of amolecule, means a chemical moiety that is not present in a naturalanalog of the molecule. For example, an exogenous label of a nucleotideis a label that is not present on a naturally occurring nucleotide.Similarly, an exogenous linker that is present on a nucleic acid is notfound on nucleic acids in their native milieu.

As used herein, “extension,” when used in reference to a nucleic acid,means a process of adding at least one nucleotide to the 3′ end of thenucleic acid. The term “polymerase extension,” when used in reference toa nucleic acid, refers to a polymerase catalyzed process of adding oneor more individual nucleotides to the 3′ end of the nucleic acid. Theterm “ligase extension,” when used in reference to a nucleic acid,refers to a ligase catalyzed process of adding at least oneoligonucleotide to the 3′ end of the nucleic acid. A nucleotide oroligonucleotide that is added to a nucleic acid by extension is said tobe incorporated into the nucleic acid. Accordingly, the term“incorporating” can be used to refer to the process of joining anucleotide or oligonucleotide to the 3′ end of a nucleic acid byformation of a phosphodiester bond.

As used herein, “extendable,” when used in reference to a nucleotide,means that the nucleotide has an oxygen or hydroxyl moiety at the 3′position, and is capable of forming a covalent linkage to a next correctnucleotide (or to an oligonucleotide) if and when incorporated into anucleic acid. An extendable nucleotide can be at the 3′ position of aprimer or it can be a monomeric nucleotide. A nucleotide that isextendable will lack blocking moieties such as reversible terminatormoieties, and a deblocked nucleotide or nucleic acid strand is oftenextendable.

As used herein, a “flow cell” is a vessel that includes one or morechannels that direct fluid to a detection zone. The detection zone canbe coupled to a detector such that a reaction occurring in the vesselcan be observed. For example, a flow cell can contain primed templatenucleic acid molecules tethered to a solid phase support, to whichnucleotides and ancillary reagents are iteratively applied and washedaway. The flow cell can include a transparent material that permits thesample to be imaged after a desired reaction occurs. For example, a flowcell can include a glass or plastic slide containing small fluidicchannels through which polymerases, dNTPs and buffers can be flowed. Theglass or plastic inside the channels can be decorated with one or moreprimed template nucleic acid molecules to be detected. An externalimaging system can be positioned to detect the molecules at a detectionzone. Exemplary flow cells, methods for their manufacture and methodsfor their use are described in US Pat. App. Publ. Nos. 2010/0111768 A1,published May 6, 2010 or 2012/0270305 A1, published Oct. 25, 2012; or WO05/065814, published Jul. 25, 2005, each of which hereby is incorporatedby reference in its entirety herein.

As used herein, “fluid” refers to a liquid or a gas, that is capable offlowing and that changes its shape to fill a vessel. In many conditions,a fluid will change shape at a steady rate when acted upon by a forcetending to change its shape. An exemplary fluid is a fluid foam which isa liquid that contains bubbles of gas. Exemplary liquids that can beused, for example, in a fluid foam include those that contain reagentsor products of a reaction such as a binding reaction, nucleic acidsequencing reaction or reaction used in an analytical assay. Aqueousliquids can be particularly useful. Exemplary gases include inert gasessuch as nitrogen (N₂) or noble gases. Useful noble gases include, forexample, helium (He), neon (Ne), argon (Ar), krypton (Kr) and xenon(Xe). Another useful gas is atmospheric air of planet earth. Furtherexamples of fluid foams and methods for making and using fluid foams areset forth in U.S. Pat. App. Ser. No. 62/883,276, which is incorporatedherein by reference.

As used herein, “halogen atom”, “halogen” or “halo” means any one of theradio-stable atoms of column 7 of the Periodic Table of the Elements,such as, fluorine, chlorine, bromine, and iodine. Additionally, termssuch as “haloalkyl” are meant to include monohaloalkyl andpolyhaloalkyl. For example, the term “halo(C₁-C₄)alkyl” includes, but isnot limited to, fluoromethyl, difluoromethyl, trifluoromethyl,2,2,2-trifluoroethyl, 4-chlorobutyl, 3-bromopropyl, and the like.

As used herein, “heterocyclyl” refers to a ring system including atleast one heteroatom (e.g., O, N, S). Such systems can be unsaturated,can include some unsaturation, or can contain some aromatic portion, orbe all aromatic. A heterocyclyl moiety may be unsubstituted orsubstituted.

As used herein, “heteroalicyclic” or “heteroalicyclyl” refers to three-,four-, five-, six-, seven-, eight-, nine-, ten-, or more up to18-membered monocyclic, bicyclic, and tricyclic ring system whereincarbon atoms together with from 1 to 5 heteroatoms constitute the ringsystem. A heterocycle may optionally contain one or more unsaturatedbonds situated in such a way, however, that a fully delocalizedpi-electron system does not occur throughout all the rings. Theheteroatoms are independently selected from oxygen, sulfur, andnitrogen. A heterocycle may further contain one or more carbonyl orthiocarbonyl functionalities, and as such the definition includesoxo-systems and thio-systems such as lactams, lactones, cyclic imides,cyclic thioimides, and cyclic carbamates. When composed of two or morerings, the rings may be joined together in a fused fashion.Additionally, any nitrogens in a heteroalicyclic moiety may bequaternized. Heteroalicyclyl or heteroalicyclic moieties may beunsubstituted or substituted. Examples of such “heteroalicyclic” or“heteroalicyclyl” moieties include but are not limited to, 1,3-dioxin,1,3-dioxane, 1,4-dioxane, 1,2-dioxolane, 1,3-dioxolane, 1,4-dioxolane,1,3-oxathiane, 1,4-oxathiin, 1,3-oxathiolane, 1,3-dithiole,1,3-dithiolane, 1,4-oxathiane, tetrahydro-1,4-thiazine, 2H-1,2-oxazine,maleimide, succinimide, barbituric acid, thiobarbituric acid,dioxopiperazine, hydantoin, dihydrouracil, trioxane,hexahydro-1,3,5-triazine, imidazoline, imidazolidine, isoxazoline,isoxazolidine, oxazoline, oxazolidine, oxazolidinone, thiazoline,thiazolidine, morpholine, oxirane, piperidine N-Oxide, piperidine,piperazine, pyrrolidine, pyrrolidone, pyrrolidione, 4-piperidone,pyrazoline, pyrazolidine, 2-oxopyrrolidine, tetrahydropyran, 4H-pyran,tetrahydrothiopyran, thiamorpholine, thiamorpholine sulfoxide,thiamorpholine sulfone, and their benzo-fused analogs (e.g.,benzimidazolidinone, tetrahydroquinoline, 3,4-methylenedioxyphenyl). Inembodiments, a fused ring heteroalicyclyl refers to multiple rings fusedtogether wherein at least one of the fused rings is a heteroalicyclylring and wherein the multiple rings are attached to the parent molecularmoiety through any atom contained within a heteroalicyclyl ring of themultiple rings. A “heteroalicyclylene,” alone or as part of anothersubstituent, means a divalent radical derived from a heteroalicyclyl.

As used herein, “heteroaryl” refers to a monocyclic or multicyclicaromatic ring system (a ring system having a least one ring with a fullydelocalized pi-electron system) that contain(s) one or more heteroatoms,that is, an element other than carbon, including but not limited to,nitrogen, oxygen, and sulfur, and at least one aromatic ring. The numberof atoms in the ring(s) of a heteroaryl moiety can vary. For example, insome embodiments, a heteroaryl moiety can contain 4 to 14 atoms in thering(s), 5 to 10 atoms in the ring(s) or 5 to 6 atoms in the ring(s).Furthermore, the term “heteroaryl” includes fused ring systems where tworings, such as at least one aryl ring and at least one heteroaryl ring,or at least two heteroaryl rings, share at least one chemical bond.Examples of heteroaryl rings include, but are not limited to, furan,furazan, thiophene, benzothiophene, phthalazine, pyrrole, oxazole,benzoxazole, 1,2,3-oxadiazole, 1,2,4-oxadiazole, thiazole,1,2,3-thiadiazole, 1,2,4-thiadiazole, benzothiazole, imidazole,benzimidazole, indole, indazole, pyrazole, benzopyrazole, isoxazole,benzoisoxazole, isothiazole, triazole, benzotriazole, thiadiazole,tetrazole, pyridine, pyridazine, pyrimidine, pyrazine, purine,pteridine, quinoline, isoquinoline, quinazoline, quinoxaline, cinnoline,and triazine. A heteroaryl moiety may be substituted or unsubstituted.In embodiments, the term “heteroaryl” includes fused ring heteroarylgroups wherein multiple rings are fused together and wherein at leastone of the fused rings is a heteroaromatic ring and wherein the multiplerings are attached to the parent molecular moiety through any atomcontained within a heteroaromatic ring of the multiple rings. A“heteroarylene,” alone or as part of another substituent, means adivalent radical derived from a heteroaryl.

As used herein, “(heteroalicyclyl)alkyl” is a heterocyclic or aheteroalicyclic moiety connected, as a substituent, via a lower alkylenemoiety. The lower alkylene and heterocyclic or a heterocyclyl of a(heteroalicyclyl)alkyl may be substituted or unsubstituted. Examplesinclude but are not limited to tetrahydro-2H-pyran-4-yl)methyl,(piperidin-4-yl)ethyl, (piperidin-4-yl)propyl,(tetrahydro-2H-thiopyran-4-yl)methyl, and (1,3-thiazinan-4-yl)methyl.

As used herein, “heteroaralkyl” and “heteroaryl(alkyl)” refer to aheteroaryl connected, as a substituent, via a lower alkylene moiety. Thelower alkylene and heteroaryl moiety of heteroaralkyl may be substitutedor unsubstituted. Examples include but are not limited to2-thienylalkyl, 3-thienylalkyl, furylalkyl, thienylalkyl, pyrrolylalkyl,pyridylalkyl, isoxazolylalkyl, and imidazolylalkyl, and theirbenzo-fused analogs.

As used herein, “hydroxy” refers to a —OH moiety. Similarly,“hydroxylated” refers to a molecule to which —OH moieties have beenadded, for example to facilitate solubility.

As used herein, “label” refers to a molecule, or moiety thereof, thatprovides a detectable characteristic. The detectable characteristic canbe, for example, an optical signal such as absorbance of radiation,fluorescence emission, luminescence emission, fluorescence lifetime,fluorescence polarization, or the like; Rayleigh and/or Mie scattering;binding affinity for a ligand or receptor, such as an antibody orstreptavidin; magnetic properties; electrical properties; conductivity;charge; mass; radioactivity or the like. Exemplary labels include,without limitation, a fluorophore, luminophore, chromophore,nanoparticle (e.g., gold, silver, carbon nanotubes), heavy atoms,radioactive isotope, mass label, charge label, spin label, receptor,ligand, or the like.

As used herein, “linker” and “linker moiety” refer to an atom or moietythat joins two different entities. Typically, a linker will provide orcomprise a covalent bond, or a series of covalent bonds, between the twoentities. However, a linker can include non-covalent bonds such as thosethat form between a receptor and ligand. Exemplary entities that can belinked include, but are not limited to, a solid support, moiety (e.g. anucleotide monomer of a nucleic acid or a base of a nucleotide) ormolecule (e.g. a nucleic acid or label).

As used herein, “next correct nucleotide” refers to the nucleotide typethat will bind and/or incorporate at the 3′ end of a primer tocomplement a base in a template strand to which the primer is hybridizedwhen correctly basepaired. The base in the template strand is referredto as the “next base” and is immediately 5′ of the base in the templatethat is hybridized to the 3′ end of the primer. The next correctnucleotide can be referred to as the “cognate” of the next base and viceversa. Cognate nucleotides that interact with each other in a ternarycomplex or in a double stranded nucleic acid are said to “pair” witheach other. In accordance with Watson-Crick pairing rules adenine (A)pairs with thymine (T) or uracil (U), and guanine (G) pairs withcytosine (C) or uracil (U). A nucleotide having a base that is notcomplementary to the next template base is referred to as an“incorrect”, “mismatch” or “non-cognate” nucleotide.

As used herein, “nucleobase” (also referred to as a “nitrogenous base”or a “base”) refers to a purine or purine derivative or pyrimidine orpyrimidine derivative that forms the differentiating unit of anucleotide. The five primary or canonical nucleobases are adenine (A),cytosine (C), guanine (G), thymine (T), and uracil (U). Adenine andguanine are purine bases. Cytosine, uracil, and thymine are pyrimidinebases. Each of the base pairs in a typical double-helix includes apurine and a pyrimidine: either an A paired with a T, an A paired with aU, or a G paired with a C or a G paired with a U. Thesepurine-pyrimidine pairs, are referred to as ‘base complements’ or aresaid to be “complementary” to each other. Cytosine nucleobases, inparticular, are subject to modification or degradation pursuant toreplacing some protecting groups with blocking groups.

As used herein, “nucleic acid” refers to at least two nucleotidescovalently linked together. Thus, an exemplary “nucleic acid” is apolynucleotide, such as DNA, RNA, or any combination thereof. Typicalnucleic acids can be acted upon by a polymerase during nucleic acidsynthesis or detection. The term “nucleic acid” includes single-,double-, or multiple-stranded DNA, RNA and analogs (derivatives)thereof.

As used herein, “nucleotide” can be used to refer to a native nucleotideor analog thereof. Generally, a nucleotide has three moieties: anucleobase (e.g. purine or pyrimidine), a five-carbon sugar (e.g. riboseor deoxyribose), and at least one phosphate. Examples include, but arenot limited to, nucleotide triphosphates (NTPs) such as ribonucleotidetriphosphates (rNTPs), deoxyribonucleotide triphosphates (dNTPs), ornon-natural analogs thereof such as dideoxyribonucleotide triphosphates(ddNTPs) or reversibly terminated nucleotide triphosphates (rtNTPs). Anucleotide can be in a monomeric form, for example, as a nucleotidetriphosphate, nucleotide diphosphate or nucleotide monophosphate. Anucleotide can also be a moiety of a nucleic acid polymer, for example,being identified according to its position in the polymer such as the 3′nucleotide (i.e. the nucleotide moiety that is present at the 3′ end ofthe polymer) or the 5′ nucleotide (i.e. the nucleotide moiety that ispresent at the 5′ end of the polymer). A nucleoside contains anucleobase and a 5-carbon sugar. Thus, a nucleotide is a nucleosidehaving a phosphate moiety.

As used herein, “optionally substituted,” when used in reference to amoiety of a molecule, means that the moiety may be unsubstituted orsubstituted with one or more of the indicated substituents. Likewise,when a moiety is described as being “substituted or unsubstituted” or“unsubstituted or substituted,” the substituent may be selected from oneor more the indicated substituents. If no substituents are indicated, itis meant that the indicated “optionally substituted” or “substituted”moiety may be individually and independently substituted with one ormore moieties individually and independently selected from a group offunctionalities including, but not limited to, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl,hydroxy, protected hydroxyl, alkoxy, aryloxy, acyl, mercapto, alkylthio,arylthio, cyano, halogen, thiocarbonyl, O-carbamyl, N-carbamyl,O-thiocarbamyl, N-thiocarbamyl, C-amido, N-amido, S-sulfonamido,N-sulfonamido, C-carboxy, protected C-carboxy, O-carboxy, isocyanato,thiocyanato, isothiocyanato, nitro, silyl, sulfenyl, sulfinyl, sulfonyl,haloalkyl, haloalkoxy, trihalomethanesulfonyl,trihalomethanesulfonamido, amino, mono-substituted amino group,di-substituted amino group, and protected derivatives thereof. If nosubstituents are indicated in reference to an “unsubstituted” moiety,the omitted moiety(ies) may individually and independently be selectedfrom a group of functionalities including, but not limited to, those setforth in the previous sentence or elsewhere herein.

Each of the above terms (e.g., “alkyl,” “alkenyl,” “alkynyl,”“heteroalkyl,” “cycloalkyl,” “cycloalkenyl,” “cycloalkynyl,”“heteroalicyclyl,” “aryl,” “heteroaryl”, “alkylene,” “alkenylene,”“alkynylene,” “heteroalkylene,” “cycloalkylene,” “cycloalkenylene,”“cycloalkynylene,” “heteroalicyclylene,” “arylene,” and “heteroarylene”)includes both substituted and unsubstituted forms of the indicatedradical. Preferred substituents for each type of radical are providedbelow.

Substituents for the alkyl and heteroalkyl radicals can be one or moreof a variety of groups selected from, but not limited to, —OR′, ═O,═NR′, ═N—OR′, —NR′R″, —SR′, -halogen, —SiR′R″R′″, —OC(O)R′, —C(O)R′,—CO₂R′, —CONR′R″, —OC(O)NR′R″, —NR″C(O)R′, —NR′C(O)NR″R′″, —NR″C(O)₂R′,—NRC(NR′R″R′″)═NR″″, —NRC(NR′R″)═NR′″, —S(O)R′, —S(O)₂R′, —S(O)₂NR′R″,—NRSO₂R′, —NR′NR″R′″, —ONR′R″, —NR′C(O)NR″NR′″R″″, —CN, —NO₂, —NR′SO₂R″,—NR′C(O)R″, —NR′C(O)OR″, —NR′OR″, —N₃, in a number ranging from zero to(2m′+1), where m′ is the total number of carbon atoms in such radical.R, R′, R″, R′″, and R″″ each preferably independently refer to hydrogen,substituted or unsubstituted heteroalkyl, substituted or unsubstitutedcycloalkyl, substituted or unsubstituted heteroalicyclyl, substituted orunsubstituted aryl (e.g., aryl substituted with 1-3 halogens),substituted or unsubstituted heteroaryl, substituted or unsubstitutedalkyl, alkoxy, or thioalkoxy groups, or arylalkyl groups. When acompound described herein includes more than one R group, for example,each of the R groups is independently selected as are each R′, R″, R′″,and R″″ group when more than one of these groups is present. When R′ andR″ are attached to the same nitrogen atom, they can be combined with thenitrogen atom to form a 4-, 5-, 6-, or 7-membered ring. For example,—NR′R″ includes, but is not limited to, 1-pyrrolidinyl and4-morpholinyl. From the above discussion of substituents, one of skillin the art will understand that the term “alkyl” is meant to includegroups including carbon atoms bound to groups other than hydrogengroups, such as haloalkyl (e.g., —CF₃ and —CH₂CF₃) and acyl (e.g.,—C(O)CH₃, —C(O)CF₃, —C(O)CH₂OCH₃, and the like).

Similar to the substituents described for the alkyl radical,substituents for the aryl and heteroaryl groups are varied and areselected from, for example: —OR′, —NR′R″, —SR′, -halogen, —SiR′R″R′″,—OC(O)R′, —C(O)R′, —CO₂R′, —CONR′R″, —OC(O)NR′R″, —NR″C(O)R′,—NR′C(O)NR″R′″, —NR″C(O)₂R′, —NRC(NR′R″R′″)═NR″″, —NRC(NR′R″)═NR′″,—S(O)R′, —S(O)₂R′, —S(O)₂NR′R″, —NRSO₂R′, —NR′NR″R′″, —ONR′R″,—NR′C(O)NR″NR′″R″″, —CN, —NO₂, —R′, —N₃, —CH(Ph)₂, fluoro(C₁-C₄)alkoxy,and fluoro(C₁-C₄)alkyl, —NR′SO₂R″, —NR′C(O)R″, —NR′C(O)—OR″, —NR′OR″, ina number ranging from zero to the total number of open valences on thearomatic ring system; and where R′, R″, R′″, and R″″ are preferablyindependently selected from hydrogen, substituted or unsubstitutedalkyl, substituted or unsubstituted alkenyl, substituted orunsubstituted alkynyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedcycloalkenyl, substituted or unsubstituted cycloalkynyl, substituted orunsubstituted heteroalicyclyl, substituted or unsubstituted aryl, andsubstituted or unsubstituted heteroaryl. When a compound describedherein includes more than one R group, for example, each of the R groupsis independently selected as are each R′, R″, R′″, and R″″ groups whenmore than one of these groups is present.

Substituents for rings (e.g., cycloalkyl, cycloalkenyl, cycloalkynyl,heteroalicyclyl, aryl, or heteroaryl) may be depicted as substituents onthe ring rather than on a specific atom of a ring (commonly referred toas a floating substituent). In such a case, the substituent may beattached to any of the ring atoms (obeying the rules of chemicalvalency) and in the case of fused rings or spirocyclic rings, asubstituent depicted as associated with one member of the fused rings orspirocyclic rings (a floating substituent on a single ring), may be asubstituent on any of the fused rings or spirocyclic rings (a floatingsubstituent on multiple rings). When a substituent is attached to aring, but not a specific atom (a floating substituent), and a subscriptfor the substituent is an integer greater than one, the multiplesubstituents may be on the same atom, same ring, different atoms,different fused rings, different spirocyclic rings, and each substituentmay optionally be different. Where a point of attachment of a ring tothe remainder of a molecule is not limited to a single atom (a floatingsubstituent), the attachment point may be any atom of the ring and inthe case of a fused ring or spirocyclic ring, any atom of any of thefused rings or spirocyclic rings while obeying the rules of chemicalvalency. Where a ring, fused rings, or spirocyclic rings contain one ormore ring heteroatoms and the ring, fused rings, or spirocyclic ringsare shown with one more floating substituents (including, but notlimited to, points of attachment to the remainder of the molecule), thefloating substituents may be bonded to the heteroatoms. Where the ringheteroatoms are shown bound to one or more hydrogens (e.g., a ringnitrogen with two bonds to ring atoms and a third bond to a hydrogen) inthe structure or formula with the floating substituent, when theheteroatom is bonded to the floating substituent, the substituent willbe understood to replace the hydrogen, while obeying the rules ofchemical valency.

Two or more substituents may optionally be joined to form aryl,heteroaryl, cycloalkyl, cycloalkenyl, cycloalkynyl, or heteroalicyclylgroups. Such so-called ring-forming substituents are typically, thoughnot necessarily, found attached to a cyclic base structure. In oneembodiment, the ring-forming substituents are attached to adjacentmembers of the base structure. For example, two ring-formingsubstituents attached to adjacent members of a cyclic base structurecreate a fused ring structure. In another embodiment, the ring-formingsubstituents are attached to a single member of the base structure. Forexample, two ring-forming substituents attached to a single member of acyclic base structure create a spirocyclic structure. In yet anotherembodiment, the ring-forming substituents are attached to non-adjacentmembers of the base structure.

As used herein, the terms “heteroatom” or “ring heteroatom” are meant toinclude oxygen (O), nitrogen (N), sulfur (S), selenium (Se), phosphorus(P), and silicon (Si).

A “substituent group,” as used herein, means a group selected from thefollowing moieties:

-   -   (A) oxo,    -   halogen, —CCl₃, —CBr₃, —CF₃, —CI₃, —CHCl₂, —CHBr₂, —CHF₂, —CHI₂,        —CH₂Cl, —CH₂Br, —CH₂F, —CH₂I, —OCCl₃, —OCF₃, —OCBr₃, —OCI₃,        —OCHCl₂, —OCHBr₂, —OCHI 2, —OCHF₂, —OCH₂Cl, —OCH₂Br, —OCH₂I,        —OCH₂F, —CN, —OH, —NH₂, —COOH, —C ONH₂, —NO₂, —SH, —SO₃H,        —OSO₃H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂,        —NHSO₂H, —NHC(O)H, —NHC(O)OH, —NHOH, —N₃, unsubstituted alkyl        (e.g., C₁-C₈ alkyl, C₁-C₆ alkyl, or C₁-C₄ alkyl), unsubstituted        alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆ alkenyl, or C₂-C₄ alkenyl),        unsubstituted alkynyl (e.g., C₂-C₈ alkynyl, C₂-C₆ alkynyl, or        C₂-C₄ alkynyl), unsubstituted heteroalkyl (e.g., 2 to 8 membered        heteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 membered        heteroalkyl), unsubstituted cycloalkyl (e.g., C₃-C₈ cycloalkyl,        C₃-C₆ cycloalkyl, or C₅-C₆ cycloalkyl), unsubstituted        cycloalkenyl (e.g., C₃-C₈ cycloalkenyl, C₃-C₆ cycloalkenyl, or        C₅-C₆ cycloalkenyl), unsubstituted cycloalkynyl (e.g., C₃-C₈        cycloalkynyl, C₃-C₆ cycloalkynyl, or C5-C6 cycloalkynyl),        unsubstituted heteroalicyclyl (e.g., 3 to 8 membered        heteroalicyclyl, 3 to 6 membered heteroalicyclyl, or 5 to 6        membered heteroalicyclyl), unsubstituted aryl (e.g., C₆-C₁₀        aryl, C₁₀ aryl, or phenyl), or unsubstituted heteroaryl (e.g., 5        to 10 membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6        membered heteroaryl), and    -   (B) alkyl (e.g., C₁-C₂₀, C₁-C₁₂, C₁-C₈, C₁-C₆, C₁-C₄, or C₁-C₂),        alkenyl (e.g., C₂-C₂₀, C₂-C₁₂, C₂-C₈, C₂-C₆, or C₂-C₄), alkynyl        (e.g., C₂-C₂₀, C₂-C₁₂, C₂-C₈, C₂-C₆, or C₂-C₄), heteroalkyl        (e.g., 2 to 20 membered, 2 to 12 membered, 2 to 8 membered, 2 to        6 membered, 4 to 6 membered, 2 to 3 membered, or 4 to 5        membered), cycloalkyl (e.g., C₃-C₁₀, C₃-C₈, C₃-C₆, C₄-C₆, or        C5-C6), cycloalkenyl (e.g., C₃-C₁₀, C₃-C₈, C₃-C₆, C₄-C₆, or        C₅-C₆), cycloalkynyl (e.g., C₃-C₁₀, C₃-C₈, C₃-C₆, C₄-C₆, or        C₅-C₆), heteroalicyclyl (e.g., 3 to 10 membered, 3 to 8        membered, 3 to 6 membered, 4 to 6 membered, 4 to 5 membered, or        5 to 6 membered), aryl (e.g., C₆-C₁₂, C₆-C₁₀, or phenyl), or        heteroaryl (e.g., 5 to 12 membered, 5 to 10 membered, 5 to 9        membered, or 5 to 6 membered), substituted with at least one        substituent selected from:        -   (i) oxo,        -   halogen, —CCl₃, —CBr₃, —CF₃, —CI₃, —CHCl₂, —CHBr₂, —CHF₂,            —CHI₂, —CH₂Cl, —C H₂Br, —CH₂F, —CH₂I, —OCCl₃, —OCF₃, —OCBr₃,            —OCI₃, —OCHCl₂, —OCHBr₂, —O CHI₂, —OCHF₂, —OCH₂Cl, —OCH₂Br,            —OCH₂I, —OCH₂F, —CN, —OH, —NH₂, —CO OH, —CONH₂, —NO₂, —SH,            —SO₃H, —OSO₃H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC(O)NHNH₂,            —NHC(O)NH₂, —NHSO₂H, —NHC(O)H, —NHC(O)OH, —NHOH, —N₃,            unsubstituted alkyl (e.g., C₁-C₈ alkyl, C₁-C₆ alkyl, or            C₁-C₄ alkyl), unsubstituted alkenyl (e.g., C₂-C₈ alkenyl,            C₂-C₆ alkenyl, or C₂-C₄ alkenyl), unsubstituted alkynyl            (e.g., C₂-C₈ alkynyl, C₂-C₆ alkynyl, or C₂-C₄ alkynyl),            unsubstituted heteroalkyl (e.g., 2 to 8 membered            heteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 membered            heteroalkyl), unsubstituted cycloalkyl (e.g., C₃-C₈            cycloalkyl, C₃-C₆ cycloalkyl, or C₅-C₆ cycloalkyl),            unsubstituted cycloalkenyl (e.g., C₃-C₈ cycloalkenyl, C₃-C₆            cycloalkenyl, or C₅-C₆ cycloalkenyl), unsubstituted            cycloalkynyl (e.g., C₃-C₈ cycloalkynyl, C₃-C₆ cycloalkynyl,            or C₅-C₆ cycloalkynyl), unsubstituted heteroalicyclyl (e.g.,            3 to 8 membered heteroalicyclyl, 3 to 6 membered            heteroalicyclyl, or 5 to 6 membered heteroalicyclyl),            unsubstituted aryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl),            or unsubstituted heteroaryl (e.g., 5 to 10 membered            heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered            heteroaryl), and        -   (ii) alkyl (e.g., C₁-C₂₀, C₁-C₁₂, C₁-C₈, C₁-C₆, C₁-C₄, or            C₁-C₂), alkenyl (e.g., C₂-C₂₀, C2-C12, C₂-C₈, C₂-C₆, or            C₂-C₄), alkynyl (e.g., C₂-C₂₀, C2-C12, C₂-C₈, C₂-C₆, or            C₂-C₄), heteroalkyl (e.g., 2 to 20 membered, 2 to 12            membered, 2 to 8 membered, 2 to 6 membered, 4 to 6 membered,            2 to 3 membered, or 4 to 5 membered), cycloalkyl (e.g.,            C₃-C₁₀, C₃-C₈, C₃-C₆, C₄-C₆, or C5-C6), cycloalkenyl (e.g.,            C₃-C₁₀, C₃-C₈, C₃-C₆, C₄-C₆, or C₅-C₆), cycloalkynyl (e.g.,            C₃-C₁₀, C₃-C₈, C₃-C₆, C₄-C₆, or C₅-C₆), heteroalicyclyl            (e.g., 3 to 10 membered, 3 to 8 membered, 3 to 6 membered, 4            to 6 membered, 4 to 5 membered, or 5 to 6 membered), aryl            (e.g., C₆-C₁₂, C₆-C₁₀, or phenyl), or heteroaryl (e.g., 5 to            12 membered, 5 to 10 membered, 5 to 9 membered, or 5 to 6            membered), substituted with at least one substituent            selected from:            -   (a) oxo,            -   halogen, —CCl₃, —CBr₃, —CF₃, —CI₃, —CHCl₂, —CHBr₂,                —CHF₂, —CHI₂, —CH₂Cl, —CH₂Br, —CH₂F, —CH₂I, —OCCl₃,                —OCF₃, —OCBr₃, —OCI₃, —OCHCl₂, —OCHBr₂, —OCHI₂, —OCHF₂,                —OCH₂Cl, —OCH₂Br, —OCH₂I, —OCH₂F, —CN, —OH, —NH 2,                —COOH, —CONH₂, —NO₂, —SH, —SO₃H, —OSO₃H, —SO₂NH₂,                —NHNH₂, —ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂, —NHSO₂H,                —NHC(O)H, —NHC(O)OH, —NHOH, —N₃, unsubstituted alkyl                (e.g., C₁-C₈ alkyl, C₁-C₆ alkyl, or C₁-C₄ alkyl),                unsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆                alkenyl, or C₂-C₄ alkenyl), unsubstituted alkynyl (e.g.,                C₂-C₈ alkynyl, C₂-C₆ alkynyl, or C2-C4 alkynyl),                unsubstituted heteroalkyl (e.g., 2 to 8 membered                heteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4                membered heteroalkyl), unsubstituted cycloalkyl (e.g.,                C₃-C₈ cycloalkyl, C₃-C₆ cycloalkyl, or C₅-C₆                cycloalkyl), unsubstituted cycloalkenyl (e.g., C₃-C₈                cycloalkenyl, C₃-C₆ cycloalkenyl, or C₅-C₆                cycloalkenyl), unsubstituted cycloalkynyl (e.g., C₃-C₈                cycloalkynyl, C₃-C₆ cycloalkynyl, or C₅-C₆                cycloalkynyl), unsubstituted heteroalicyclyl (e.g., 3 to                8 membered heteroalicyclyl, 3 to 6 membered                heteroalicyclyl, or 5 to 6 membered heteroalicyclyl),                unsubstituted aryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, or                phenyl), or unsubstituted heteroaryl (e.g., 5 to 10                membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to                6 membered heteroaryl), and            -   (b) alkyl (e.g., C₁-C₂₀, C₁-C₁₂, C₁-C₈, C₁-C₆, C₁-C₄, or                C₁-C₂), alkenyl (e.g., C₂-C₂₀, C₂-C₁₂, C₂-C₈, C₂-C₆, or                C₂-C₄), alkynyl (e.g., C₂-C₂₀, C2-C12, C₂-C₈, C₂-C₆, or                C₂-C₄), heteroalkyl (e.g., 2 to 20 membered, 2 to 12                membered, 2 to 8 membered, 2 to 6 membered, 4 to 6                membered, 2 to 3 membered, or 4 to 5 membered),                cycloalkyl (e.g., C₃-C₁₀, C₃-C₈, C₃-C₆, C₄-C₆, or                C₅-C₆), cycloalkenyl (e.g., C₃-C₁₀, C₃-C₈, C₃-C₆, C₄-C₆,                or C5-C6), cycloalkynyl (e.g., C₃-C₁₀, C₃-C₈, C₃-C₆,                C₄-C₆, or C₅-C₆), heteroalicyclyl (e.g., 3 to 10                membered, 3 to 8 membered, 3 to 6 membered, 4 to 6                membered, 4 to 5 membered, or 5 to 6 membered), aryl                (e.g., C₆-C₁₂, C₆-C₁₀, or phenyl), or heteroaryl (e.g.,                5 to 12 membered, 5 to 10 membered, 5 to 9 membered, or                5 to 6 membered), substituted with at least one                substituent selected from: oxo, halogen, —CCl₃, —CBr₃,                —CF₃, —CI₃, —CHCl₂, —CHBr₂, —CHF₂, —CHI₂, —CH₂Cl,                —CH₂Br, —CH₂F, —CH₂I, —OCCl₃, —OCF₃, —OCBr₃, —OCI₃,                —OCHCl₂, —OCHBr 2, —OCHI₂, —OCHF₂, —OCH₂Cl, —OCH₂Br,                —OCH₂I, —OCH₂F, —CN, —OH, —NH 2, —COOH, —CONH₂, —NO₂,                —SH, —SO₃H, —OSO₃H, —SO₂NH₂, —NHNH₂, —ONH₂,                —NHC(O)NHNH₂, —NHC(O)NH₂, —NHSO₂H, —NHC(O)H, —NHC(O)OH,                —NHOH, —N₃, unsubstituted alkyl (e.g., C₁-C₈ alkyl,                C₁-C₆ alkyl, or C₁-C₄ alkyl), unsubstituted alkenyl                (e.g., C₂-C₈ alkenyl, C₂-C₆ alkenyl, or C₂-C₄ alkenyl),                unsubstituted alkynyl (e.g., C₂-C₈ alkynyl, C₂-C₆                alkynyl, or C2-C4 alkynyl), unsubstituted heteroalkyl                (e.g., 2 to 8 membered heteroalkyl, 2 to 6 membered                heteroalkyl, or 2 to 4 membered heteroalkyl),                unsubstituted cycloalkyl (e.g., C₃-C₈ cycloalkyl, C₃-C₆                cycloalkyl, or C₅-C₆ cycloalkyl), unsubstituted                cycloalkenyl (e.g., C₃-C₈ cycloalkenyl, C₃-C₆                cycloalkenyl, or C₅-C₆ cycloalkenyl), unsubstituted                cycloalkynyl (e.g., C₃-C₈ cycloalkynyl, C₃-C₆                cycloalkynyl, or C₅-C₆ cycloalkynyl), unsubstituted                heteroalicyclyl (e.g., 3 to 8 membered heteroalicyclyl,                3 to 6 membered heteroalicyclyl, or 5 to 6 membered                heteroalicyclyl), unsubstituted aryl (e.g., C₆-C₁₀ aryl,                C₁₀ aryl, or phenyl), or unsubstituted heteroaryl (e.g.,                5 to 10 membered heteroaryl, 5 to 9 membered heteroaryl,                or 5 to 6 membered heteroaryl).

A “size-limited substituent” or “size-limited substituent group,” asused herein, means a group selected from all of the substituentsdescribed above for a “substituent group,” wherein each substituted orunsubstituted alkyl is a substituted or unsubstituted C₁-C₂₀ alkyl, eachsubstituted or unsubstituted alkenyl is a substituted or unsubstitutedC₂-C₂₀ alkenyl, each substituted or unsubstituted alkynyl is asubstituted or unsubstituted C₂-C₂₀ alkynyl, each substituted orunsubstituted heteroalkyl is a substituted or unsubstituted 2 to 20membered heteroalkyl, each substituted or unsubstituted cycloalkyl is asubstituted or unsubstituted C₃-C₈ cycloalkyl, each substituted orunsubstituted cycloalkenyl is a substituted or unsubstituted C₃-C₈cycloalkenyl, each substituted or unsubstituted cycloalkynyl is asubstituted or unsubstituted C₃-C₈ cycloalkynyl, each substituted orunsubstituted heteroalicyclyl is a substituted or unsubstituted 3 to 8membered heteroalicyclyl, each substituted or unsubstituted aryl is asubstituted or unsubstituted C₆-C₁₀ aryl, and each substituted orunsubstituted heteroaryl is a substituted or unsubstituted 5 to 10membered heteroaryl.

A “lower substituent” or “lower substituent group,” as used herein,means a group selected from all of the substituents described above fora “substituent group,” wherein each substituted or unsubstituted alkylis a substituted or unsubstituted C₁-C₈ alkyl, each substituted orunsubstituted alkenyl is a substituted or unsubstituted C₂-C₈ alkenyl,each substituted or unsubstituted alkynyl is a substituted orunsubstituted C₂-C₈ alkynyl, each substituted or unsubstitutedheteroalkyl is a substituted or unsubstituted 2 to 8 memberedheteroalkyl, each substituted or unsubstituted cycloalkyl is asubstituted or unsubstituted C₃-C₇ cycloalkyl, each substituted orunsubstituted cycloalkenyl is a substituted or unsubstituted C₃-C₇cycloalkenyl, each substituted or unsubstituted cycloalkynyl is asubstituted or unsubstituted C₃-C₇ cycloalkynyl, each substituted orunsubstituted heteroalicyclyl is a substituted or unsubstituted 3 to 7membered heteroalicyclyl, each substituted or unsubstituted aryl is asubstituted or unsubstituted C₆-C₁₀ aryl, and each substituted orunsubstituted heteroaryl is a substituted or unsubstituted 5 to 9membered heteroaryl.

In some embodiments, each substituted group described in the compoundsherein is substituted with at least one substituent group. Morespecifically, in some embodiments, each substituted alkyl, substitutedalkenyl, substituted alkynyl, substituted heteroalkyl, substitutedcycloalkyl, substituted cycloalkenyl, substituted cycloalkynyl,substituted heteroalicyclyl, substituted aryl, substituted heteroaryl,substituted alkylene, substituted heteroalkylene, substitutedcycloalkylene, substituted heteroalicyclylene, substituted arylene,and/or substituted heteroarylene described in the compounds herein aresubstituted with at least one substituent group. In other embodiments,at least one or all of these groups are substituted with at least onesize-limited substituent group. In other embodiments, at least one orall of these groups are substituted with at least one lower substituentgroup.

In other embodiments of the compounds herein, each substituted orunsubstituted alkyl may be a substituted or unsubstituted C₁-C₂₀ alkyl,each substituted or unsubstituted alkenyl may be a substituted orunsubstituted C₂-C₂₀ alkenyl, each substituted or unsubstituted alkynylmay be a substituted or unsubstituted C₂-C₂₀ alkynyl, each substitutedor unsubstituted heteroalkyl is a substituted or unsubstituted 2 to 20membered heteroalkyl, each substituted or unsubstituted cycloalkyl is asubstituted or unsubstituted C₃-C₈ cycloalkyl, each substituted orunsubstituted cycloalkenyl is a substituted or unsubstituted C₃-C₈cycloalkenyl, each substituted or unsubstituted cycloalkynyl is asubstituted or unsubstituted C₃-C₈ cycloalkynyl, each substituted orunsubstituted heteroalicyclyl is a substituted or unsubstituted 3 to 8membered heteroalicyclyl, each substituted or unsubstituted aryl is asubstituted or unsubstituted C₆-C₁₀ aryl, and/or each substituted orunsubstituted heteroaryl is a substituted or unsubstituted 5 to 10membered heteroaryl. In some embodiments of the compounds herein, eachsubstituted or unsubstituted alkylene is a substituted or unsubstitutedC₁-C₂₀ alkylene, each substituted or unsubstituted alkenylene is asubstituted or unsubstituted C₂-C₂₀ alkenylene, each substituted orunsubstituted alkynylene is a substituted or unsubstituted C₂-C₂₀alkynylene, each substituted or unsubstituted heteroalkylene is asubstituted or unsubstituted 2 to 20 membered heteroalkylene, eachsubstituted or unsubstituted cycloalkylene is a substituted orunsubstituted C₃-C₈ cycloalkylene, each substituted or unsubstitutedcycloalkenylene is a substituted or unsubstituted C₃-C₈ cycloalkenylene,each substituted or unsubstituted cycloalkynylene is a substituted orunsubstituted C₃-C₈ cycloalkynylene, each substituted or unsubstitutedheteroalicyclylene is a substituted or unsubstituted 3 to 8 memberedheteroalicyclylene, each substituted or unsubstituted arylene is asubstituted or unsubstituted C₆-C₁₀ arylene, and/or each substituted orunsubstituted heteroarylene is a substituted or unsubstituted 5 to 10membered heteroarylene.

In some embodiments, each substituted or unsubstituted alkyl is asubstituted or unsubstituted C₁-C₈ alkyl, each substituted orunsubstituted alkenyl is a substituted or unsubstituted C₂-C₈ alkenyl,each substituted or unsubstituted alkynyl is a substituted orunsubstituted C₂-C₈ alkynyl, each substituted or unsubstitutedheteroalkyl is a substituted or unsubstituted 2 to 8 memberedheteroalkyl, each substituted or unsubstituted cycloalkyl is asubstituted or unsubstituted C₃-C₇ cycloalkyl, each substituted orunsubstituted cycloalkenyl is a substituted or unsubstituted C₃-C₇cycloalkenyl, each substituted or unsubstituted cycloalkynyl is asubstituted or unsubstituted C₃-C₇ cycloalkynyl, each substituted orunsubstituted heteroalicyclyl is a substituted or unsubstituted 3 to 7membered heteroalicyclyl, each substituted or unsubstituted aryl is asubstituted or unsubstituted C₆-C₁₀ aryl, and/or each substituted orunsubstituted heteroaryl is a substituted or unsubstituted 5 to 9membered heteroaryl. In some embodiments, each substituted orunsubstituted alkylene is a substituted or unsubstituted C₁-C₈ alkylene,each substituted or unsubstituted alkenylene is a substituted orunsubstituted C₂-C₈ alkenylene, each substituted or unsubstitutedalkynylene is a substituted or unsubstituted C₂-C₈ alkynylene, eachsubstituted or unsubstituted heteroalkylene is a substituted orunsubstituted 2 to 8 membered heteroalkylene, each substituted orunsubstituted cycloalkylene is a substituted or unsubstituted C₃-C₇cycloalkylene, each substituted or unsubstituted cycloalkenylene is asubstituted or unsubstituted C₃-C₇ cycloalkenylene, each substituted orunsubstituted cycloalkynylene is a substituted or unsubstituted C₃-C₇cycloalkynylene, each substituted or unsubstituted heteroalicyclylene isa substituted or unsubstituted 3 to 7 membered heteroalicyclylene, eachsubstituted or unsubstituted arylene is a substituted or unsubstitutedC₆-C₁₀ arylene, and/or each substituted or unsubstituted heteroaryleneis a substituted or unsubstituted 5 to 9 membered heteroarylene. In someembodiments, the compound is a chemical species set forth in theapplication (e.g., Examples section, figures, or tables below).

In embodiments, a substituted or unsubstituted moiety (e.g., substitutedor unsubstituted alkyl, substituted or unsubstituted alkenyl,substituted or unsubstituted alkynyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted cycloalkenyl, substituted or unsubstituted cycloalkynyl,substituted or unsubstituted heteroalicyclyl, substituted orunsubstituted aryl, substituted or unsubstituted heteroaryl, substitutedor unsubstituted alkylene, substituted or unsubstituted alkenylene,substituted or unsubstituted alkynylene, substituted or unsubstitutedheteroalkylene, substituted or unsubstituted cycloalkylene, substitutedor unsubstituted cycloalkenylene, substituted or unsubstitutedcycloalkynylene, substituted or unsubstituted heteroalicyclylene,substituted or unsubstituted arylene, and/or substituted orunsubstituted heteroarylene) is unsubstituted (e.g., is an unsubstitutedalkyl, unsubstituted alkenyl, unsubstituted alkynyl, unsubstitutedheteroalkyl, unsubstituted cycloalkyl, unsubstituted cycloalkenyl,unsubstituted cycloalkynyl, unsubstituted heteroalicyclyl, unsubstitutedaryl, unsubstituted heteroaryl, unsubstituted alkylene, unsubstitutedalkenylene, unsubstituted alkynylene, unsubstituted heteroalkylene,unsubstituted cycloalkylene, unsubstituted cycloalkenylene,unsubstituted cycloalkynylene, unsubstituted heteroalicyclylene,unsubstituted arylene, and/or unsubstituted heteroarylene,respectively). In embodiments, a substituted or unsubstituted moiety(e.g., substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted cycloalkenyl, substituted or unsubstitutedcycloalkynyl, substituted or unsubstituted heteroalicyclyl, substitutedor unsubstituted aryl, substituted or unsubstituted heteroaryl,substituted or unsubstituted alkylene, substituted or unsubstitutedalkenylene, substituted or unsubstituted alkynylene, substituted orunsubstituted heteroalkylene, substituted or unsubstitutedcycloalkylene, substituted or unsubstituted cycloalkenylene, substitutedor unsubstituted cycloalkynylene, substituted or unsubstitutedheteroalicyclylene, substituted or unsubstituted arylene, and/orsubstituted or unsubstituted heteroarylene) is substituted (e.g., is asubstituted alkyl, substituted alkenyl, substituted alkynyl, substitutedheteroalkyl, substituted cycloalkyl, substituted cycloalkenyl,substituted cycloalkynyl, substituted heteroalicyclyl, substituted aryl,substituted heteroaryl, substituted alkylene, substituted alkenylene,substituted alkynylene, substituted heteroalkylene, substitutedcycloalkylene, substituted cycloalkenylene, substituted cycloalkynylene,substituted heteroalicyclylene, substituted arylene, and/or substitutedheteroarylene, respectively).

In embodiments, a substituted moiety (e.g., substituted alkyl,substituted alkenyl, substituted alkynyl, substituted heteroalkyl,substituted cycloalkyl, substituted cycloalkenyl, substitutedcycloalkynyl, substituted heteroalicyclyl, substituted aryl, substitutedheteroaryl, substituted alkylene, substituted alkenylene, substitutedalkynylene, substituted heteroalkylene, substituted cycloalkylene,substituted cycloalkenylene, substituted cycloalkynylene, substitutedheteroalicyclylene, substituted arylene, and/or substitutedheteroarylene) is substituted with at least one substituent group,wherein if the substituted moiety is substituted with a plurality ofsubstituent groups, each substituent group may optionally be different.In embodiments, if the substituted moiety is substituted with aplurality of substituent groups, each substituent group is different.

In embodiments, a substituted moiety (e.g., substituted alkyl,substituted alkenyl, substituted alkynyl, substituted heteroalkyl,substituted cycloalkyl, substituted cycloalkenyl, substitutedcycloalkynyl, substituted heteroalicyclyl, substituted aryl, substitutedheteroaryl, substituted alkylene, substituted alkenylene, substitutedalkynylene, substituted heteroalkylene, substituted cycloalkylene,substituted cycloalkenylene, substituted cycloalkynylene, substitutedheteroalicyclylene, substituted arylene, and/or substitutedheteroarylene) is substituted with at least one size-limited substituentgroup, wherein if the substituted moiety is substituted with a pluralityof size-limited substituent groups, each size-limited substituent groupmay optionally be different. In embodiments, if the substituted moietyis substituted with a plurality of size-limited substituent groups, eachsize-limited substituent group is different.

In embodiments, a substituted moiety (e.g., substituted alkyl,substituted alkenyl, substituted alkynyl, substituted heteroalkyl,substituted cycloalkyl, substituted cycloalkenyl, substitutedcycloalkynyl, substituted heteroalicyclyl, substituted aryl, substitutedheteroaryl, substituted alkylene, substituted alkenylene, substitutedalkynylene, substituted heteroalkylene, substituted cycloalkylene,substituted cycloalkenylene, substituted cycloalkynylene, substitutedheteroalicyclylene, substituted arylene, and/or substitutedheteroarylene) is substituted with at least one lower substituent group,wherein if the substituted moiety is substituted with a plurality oflower substituent groups, each lower substituent group may optionally bedifferent. In embodiments, if the substituted moiety is substituted witha plurality of lower substituent groups, each lower substituent group isdifferent.

In embodiments, a substituted moiety (e.g., substituted alkyl,substituted alkenyl, substituted alkynyl, substituted heteroalkyl,substituted cycloalkyl, substituted cycloalkenyl, substitutedcycloalkynyl, substituted heteroalicyclyl, substituted aryl, substitutedheteroaryl, substituted alkylene, substituted alkenylene, substitutedalkynylene, substituted heteroalkylene, substituted cycloalkylene,substituted cycloalkenylene, substituted cycloalkynylene, substitutedheteroalicyclylene, substituted arylene, and/or substitutedheteroarylene) is substituted with at least one substituent group,size-limited substituent group, or lower substituent group; wherein ifthe substituted moiety is substituted with a plurality of groupsselected from substituent groups, size-limited substituent groups, andlower substituent groups; each substituent group, size-limitedsubstituent group, and/or lower substituent group may optionally bedifferent. In embodiments, if the substituted moiety is substituted witha plurality of groups selected from substituent groups, size-limitedsubstituent groups, and lower substituent groups; each substituentgroup, size-limited substituent group, and/or lower substituent group isdifferent.

Certain compounds of the present disclosure possess asymmetric carbonatoms (optical or chiral centers) or double bonds; the enantiomers,racemates, diastereomers, tautomers, geometric isomers, stereoisometricforms that may be defined, in terms of absolute stereochemistry, as (R)-or (S)- or, as (D)- or (L)- for amino acids, and individual isomers areencompassed within the scope of the present disclosure. The compounds ofthe present disclosure do not include those that are known in art to betoo unstable to synthesize and/or isolate. The present disclosure ismeant to include compounds in racemic and optically pure forms.Optically active (R)- and (S)-, or (D)- and (L)-isomers may be preparedusing chiral synthons or chiral reagents, or resolved using conventionaltechniques. When the compounds described herein contain olefinic bondsor other centers of geometric asymmetry, and unless specified otherwise,it is intended that the compounds include both E and Z geometricisomers.

As used herein, the term “isomers” refers to compounds having the samenumber and kind of atoms, and hence the same molecular weight, butdiffering in respect to the structural arrangement or configuration ofthe atoms.

The term “tautomer,” as used herein, refers to one of two or morestructural isomers which exist in equilibrium and which are readilyconverted from one isomeric form to another.

It will be apparent to one skilled in the art that certain compounds ofthis disclosure may exist in tautomeric forms, all such tautomeric formsof the compounds being within the scope of the disclosure.

Unless otherwise stated, structures depicted herein are also meant toinclude all stereochemical forms of the structure; i.e., the R and Sconfigurations for each asymmetric center. Therefore, singlestereochemical isomers as well as enantiomeric and diastereomericmixtures of the present compounds are within the scope of thedisclosure.

Unless otherwise stated, structures depicted herein are also meant toinclude compounds which differ only in the presence of one or moreisotopically enriched atoms. For example, compounds having the presentstructures except for the replacement of a hydrogen by a deuterium ortritium, or the replacement of a carbon by ¹³C- or ¹⁴C-enriched carbonare within the scope of this disclosure.

The compounds of the present disclosure may also contain unnaturalproportions of atomic isotopes at one or more of the atoms thatconstitute such compounds. For example, the compounds may beradiolabeled with radioactive isotopes, such as for example tritium(³H), iodine-125 (¹²⁵I), or carbon-14 (¹⁴C). All isotopic variations ofthe compounds of the present disclosure, whether radioactive or not, areencompassed within the scope of the present disclosure.

It should be noted that throughout the application that alternatives arewritten in Markush groups, for example, each amino acid position thatcontains more than one possible amino acid. It is specificallycontemplated that each member of the Markush group should be consideredseparately, thereby comprising another embodiment, and the Markush groupis not to be read as a single unit.

“Analog” or “analogue” is used in accordance with its plain ordinarymeaning within Chemistry and Biology and refers to a chemical compoundthat is structurally similar to another compound (i.e., a so-called“reference” compound) but differs in composition, e.g., in thereplacement of one atom by an atom of a different element, or in thepresence of a particular functional group, or the replacement of onefunctional group by another functional group, or the absolutestereochemistry of one or more chiral centers of the reference compound.Accordingly, an analog is a compound that is similar or comparable infunction and appearance but not in structure or origin to a referencecompound.

The terms “a” or “an”, as used in herein means one or more. In addition,the phrase “substituted with a[n]”, as used herein, means the specifiedgroup may be substituted with one or more of any or all of the namedsubstituents. For example, where a group, such as an alkyl or heteroarylgroup, is “substituted with an unsubstituted C₁-C₂₀ alkyl, orunsubstituted 2 to 20 membered heteroalkyl”, the group may contain oneor more unsubstituted C₁-C₂₀ alkyls, and/or one or more unsubstituted 2to 20 membered heteroalkyls.

As used herein, the term “about” means a range of values including thespecified value, which a person of ordinary skill in the art wouldconsider reasonably similar to the specified value. In embodiments,about means within a standard deviation using measurements generallyacceptable in the art. In embodiments, about means a range extending to+/−10% of the specified value. In embodiments, about includes thespecified value.

In this disclosure, “comprises”, “comprising”, “containing”, and“having” and the like can have the meaning ascribed to them in U.S.Patent law and can mean “includes”, “including”, and the like.“Consisting essentially of” or “consists essentially” likewise has themeaning ascribed in U.S. Patent law and the term is open-ended, allowingfor the presence of more than that which is recited so long as basic ornovel characteristics of that which is recited is not changed by thepresence of more than that which is recited, but excludes prior artembodiments.

Moreover, where a moiety is substituted with an R substituent, the groupmay be referred to as “R-substituted.” Where a moiety is R-substituted,the moiety is substituted with at least one R substituent and each Rsubstituent is optionally different. Where a particular R group ispresent in the description of a chemical genus (such as Formula (I)), aRoman alphabetic symbol may be used to distinguish each appearance ofthat particular R group. For example, where multiple R¹³ substituentsare present, each R¹³ substituent may be distinguished as R^(13A),R^(13B), R^(13C), R^(13D), etc., wherein each of R^(13A), R^(13B),R^(13C), R^(13D), etc. is defined within the scope of the definition ofR¹³ and optionally differently.

A “detectable agent” or “detectable moiety” is a substance, element,compound, or composition; or moiety thereof, detectable by appropriatemeans such as spectroscopic, photochemical, biochemical, immunochemical,chemical, magnetic resonance imaging, or other physical means. Forexample, useful detectable agents include ¹⁸F, ³²P, ³³P, ⁴⁵Ti, ⁴⁷Sc,⁵²Fe, ⁹Fe ⁶²Cu, ⁶⁴Cu, ⁶⁷Cu, ⁶⁷Ga ⁶⁸Ga, ⁷⁷As, ⁸⁶Y, ⁹⁰Y, ⁸⁹Sr, ⁸⁹Zr, ⁹⁴Tc,⁹⁴Tc, ^(99m)Tc, ⁹⁹Mo, ¹⁰⁵Pd, ¹⁰⁵Ph, ¹¹¹Ag, ¹¹¹In, ¹²³I, ¹²⁴I, ¹²⁵I,¹³¹I, ¹⁴²Pr, ¹⁴³Pr, ¹⁴⁹Pm, ¹⁵³Sm, ¹⁵⁴⁻¹⁵⁸¹Gd, ¹⁶¹Tb, ¹⁶⁶Dy, ¹⁶⁶Ho,¹⁶⁹Er, ¹⁷⁵Lu, ¹⁷⁷Lu, ¹⁸⁶Re, ⁸⁸Re, ¹⁸⁹Re, ¹⁹⁴Ir, ¹⁹⁸Au, ¹⁹⁹Au, ²¹¹At,²¹¹Pb, ²¹²Bi, ²¹²Pb, ²¹³Bi, ²²³Ra, ²²⁵Ac, Cr, V, Mn, Fe, Co, Ni, Cu, La,Ce, Pr, Nd, Pm, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, ³²P, fluorophore(e.g., fluorescent dyes), electron-dense reagents, enzymes (e.g., ascommonly used in an ELISA), biotin, digoxigenin, paramagnetic molecules,paramagnetic nanoparticles, ultrasmall superparamagnetic iron oxide(“USPIO”) nanoparticles, USPIO nanoparticle aggregates,superparamagnetic iron oxide (“SPIO”) nanoparticles, SPIO nanoparticleaggregates, monochrystalline iron oxide nanoparticles, monochrystallineiron oxide, nanoparticle contrast agents, liposomes or other deliveryvehicles containing Gadolinium chelate (“Gd-chelate”) molecules,Gadolinium, radioisotopes, radionuclides (e.g., carbon-11, nitrogen-13,oxygen-15, fluorine-18, rubidium-82), fluorodeoxyglucose (e.g.,fluorine-18 labeled), any gamma ray emitting radionuclides,positron-emitting radionuclide, radiolabeled glucose, radiolabeledwater, radiolabeled ammonia, biocolloids, microbubbles (e.g., includingmicrobubble shells including albumin, galactose, lipid, and/or polymers;microbubble gas core including air, heavy gas(es), perfluorcarbon,nitrogen, octafluoropropane, perflexane lipid microsphere, perflutren,etc.), iodinated contrast agents (e.g., iohexol, iodixanol, ioversol,iopamidol, ioxilan, iopromide, diatrizoate, metrizoate, ioxaglate),barium sulfate, thorium dioxide, gold, gold nanoparticles, goldnanoparticle aggregates, fluorophores, two-photon fluorophores, orhaptens and proteins or other entities which can be made detectable,e.g., by incorporating a radiolabel into a peptide specifically reactivewith a target peptide. A detectable moiety is a monovalent detectableagent or a detectable agent capable of forming a bond with anothercomposition.

Radioactive substances (e.g., radioisotopes) that may be used as imagingand/or labeling agents in accordance with the embodiments of thedisclosure include, but are not limited to, ¹⁸F, ³²P, ³³P, ⁴⁵Ti, ⁴⁷Sc,⁵²Fe, ⁵⁹Fe, ⁶²Cu, ⁶⁴Cu, ⁶⁷Cu, ⁶⁷Ga ⁶⁸Ga, ⁷⁷As, ⁸⁶Y, ⁹⁰Y, ⁸⁹Sr, ⁸⁹Zr,⁹⁴Tc, ⁹⁴Tc, ^(99m)Tc, ⁹⁹Mo, ¹⁰⁵Pd, ¹⁰⁵Ph, ¹¹¹Ag, ¹¹¹In, ¹²³I, ¹²⁴I,¹²⁵I, ¹³¹I, ¹⁴²Pr, ¹⁴³Pr, ¹⁴⁹Pm, ¹⁵³Sm, ¹⁵⁴⁻¹⁵⁸Gd, ¹⁶¹Tb, ¹⁶⁶Dy, ¹⁶⁶Ho,¹⁶⁹Er, ¹⁷⁵Lu, ¹⁷⁷Lu, ¹⁸⁶Re, ¹⁸⁸Re ¹⁸⁹Re, ¹⁹⁴Ir, ¹⁹⁸Au, ¹⁹⁹Au, ²¹¹At,²¹¹Pb, ²¹²Bi, ²¹²Pb, ²¹³Bi, ²²³Ra, and ²²⁵Ac. Paramagnetic ions that maybe used as additional imaging agents in accordance with the embodimentsof the disclosure include, but are not limited to, ions of transitionand lanthanide metals (e.g., metals having atomic numbers of 21-29, 42,43, 44, or 57-71). These metals include ions of Cr, V, Mn, Fe, Co, Ni,Cu, La, Ce, Pr, Nd, Pm, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu.

The terms “polypeptide”, “peptide”, and “protein” are usedinterchangeably herein to refer to a polymer of amino acid residues,wherein the polymer may optionally be conjugated to a moiety that doesnot consist of amino acids. The terms apply to amino acid polymers inwhich one or more amino acid residue is an artificial chemical mimeticof a corresponding naturally occurring amino acid, as well as tonaturally occurring amino acid polymers and non-naturally occurringamino acid polymer.

As used herein, “oxime” refers to a moiety having the followingstructure:

The oxime moiety can be attached to another moiety via the oxygen atomin which case the moiety can be referred to as an “O-oxime” moiety. Analdoxime moiety will have a hydrogen at one of R or R′. A ketoxime willhave hydrogen at neither R nor R′. Oximes are exemplary protectinggroups in some embodiments disclosed herein. A 3′-O-oxime is an oximemoiety attached to the 3′ carbon of a nucleotide or nucleoside throughthe oxime oxygen.

As used herein, “polymerase” can be used to refer to a nucleic acidsynthesizing enzyme, including but not limited to, DNA polymerase, RNApolymerase, reverse transcriptase, primase and transferase. Typically,the polymerase has one or more active sites at which nucleotide bindingand/or catalysis of nucleotide polymerization may occur. The polymerasemay catalyze the polymerization of nucleotides to the 3′ end of thefirst strand of the double stranded nucleic acid molecule. For example,a polymerase can catalyze the addition of a next correct nucleotide tothe 3′ oxygen group of the first strand of the double stranded nucleicacid molecule via a phosphodiester bond, thereby covalentlyincorporating the nucleotide to the first strand of the double strandednucleic acid molecule. Optionally, a polymerase need not be capable ofnucleotide incorporation under one or more conditions used in a methodset forth herein. For example, a mutant polymerase may be capable offorming a ternary complex but incapable of catalyzing nucleotideincorporation.

As used herein, “primed template nucleic acid” or “primed template”refers to a nucleic acid having a double stranded region such that oneof the strands is a primer and the other strand is a template. The twostrands can be parts of a contiguous nucleic acid molecule (e.g. ahairpin structure) or the two strands can be separable molecules thatare not covalently attached to each other.

As used herein, “primer” refers to a nucleic acid having a sequence thatbinds to a nucleic acid at or near a template sequence. In particularconfigurations, the primer binds in a configuration that allowsreplication of the template, for example, via polymerase extension ofthe primer or ligase extension of the primer. The primer can be a firstportion of a nucleic acid molecule that binds to a second portion of thenucleic acid molecule, the first portion being a primer sequence and thesecond portion being a primer binding sequence (e.g. a hairpin primer).Alternatively, the primer can be a first nucleic acid molecule thatbinds to a second nucleic acid molecule having the template sequence. Aprimer can consist of DNA, RNA or analogs thereof. A primer can have anextendible 3′ end or a 3′ end that is blocked, such as reversiblyterminated, so as to preclude primer extension until removal of theblocking moiety.

As used herein, “site,” when used in reference to an array, means alocation in an array where a particular molecule is present. A site cancontain only a single molecule or it can contain a population of severalmolecules of the same species (e.g. an ensemble of the molecules).Alternatively, a site can include a population of molecules that aredifferent species (e.g. a population of different template sequences).Sites of an array are typically discrete. The discrete sites can becontiguous or they can have spaces between each other. An array usefulherein can have, for example, sites that are separated by less than 100microns, 50 microns, 10 microns, 5 microns, 1 micron, or 0.5 micron.Alternatively or additionally, an array can have sites that areseparated by greater than 0.5 micron, 1 micron, 5 microns, 10 microns,50 microns or 100 microns. The sites can each have an area of less than1 square millimeter, 500 square microns, 100 square microns, 25 squaremicrons, 1 square micron or less. The density of sites of sites in anarray can be, for example, at least about 10 sites/cm², 100 sites/cm²,1×10³ sites/cm², 1×10⁴ sites/cm², 1×10⁵ sites/cm², 1×10⁶ sites/cm², orhigher.

As used herein, “solid support” or “solid phase support” refers to arigid substrate that is insoluble in aqueous liquid. The substrate canbe non-porous or porous. The substrate can optionally be capable oftaking up a liquid (e.g. due to porosity) but will typically besufficiently rigid that the substrate does not swell substantially whentaking up the liquid and does not contract substantially when the liquidis removed by drying. A nonporous solid support is generally impermeableto liquids or gases. Exemplary solid supports include, but are notlimited to, glass and modified or functionalized glass, plastics(including acrylics, polystyrene and copolymers of styrene and othermaterials, polypropylene, polyethylene, polybutylene, polyurethanes,Teflon™, cyclic olefins, polyimides etc.), nylon, ceramics, resins,Zeonor, silica or silica-based materials including silicon and modifiedsilicon, carbon, metals, inorganic glasses, optical fiber bundles, andpolymers.

As used herein, the term “surface” refers to a portion of a solidsupport that contacts a fluid. The fluid can be gas or liquid. Thesurface can be substantially flat or planar. Alternatively, the surfacecan be rounded or contoured. Exemplary contours that can be included ona surface are wells, depressions, pillars, ridges, channels or the like.Exemplary materials that can be used as a solid support include, but arenot limited to, those set forth above.

As used herein, “ternary complex” refers to an intermolecularassociation between a polymerase, a double stranded nucleic acid and anucleotide. Typically, the polymerase facilitates interaction between anext correct nucleotide and a template strand of the primed nucleicacid. A next correct nucleotide can interact with the template strandvia Watson-Crick hydrogen bonding. The term “stabilized ternary complex”means a ternary complex having promoted or prolonged existence or aternary complex for which disruption has been inhibited. Generally,stabilization of the ternary complex prevents covalent incorporation ofthe nucleotide component of the ternary complex into the primed nucleicacid component of the ternary complex.

As used herein, “type” is used to identify molecules that share the samechemical structure. For example, a mixture of nucleotides can includeseveral dCTP molecules. The dCTP molecules will be understood to be thesame type of nucleotide as each other, but a different type ofnucleotide compared to dATP, dGTP, dTTP etc. Similarly, individual DNAmolecules that have the same sequence of nucleotides are the same type,whereas DNA molecules with different sequences are different types. Theterm “type” can also identify moieties that share the same chemicalstructure. For example, the cytosine bases in a template nucleic acidwill be understood to be the same type of base as each other independentof their position in the template sequence.

As used herein, a “vessel” is a container that functions to isolate onechemical process (e.g., a binding event; an incorporation reaction;addition of a nucleotide to an extending chain, removal of a reversibleterminator from a 3′ end of a blocked nucleotide or extending primer; orreplacement of a protecting moiety by a blocking moiety; or otherreaction such as a reaction involving nucleic acid chemistry) fromanother, or to provide a space in which a chemical process can takeplace. Non-limiting examples of vessels useful in connection with thedisclosed technique include: flow cells, wells of a multi-well plate;microscope slides; tubes (e.g., capillary tubes); droplets, vesicles,test tubes, trays, centrifuge tubes, features in an array, tubing,channels in a substrate or other volumes used in nucleic acid chemistry.As used herein, a “manufactured vessel” is a container that ishuman-made or human-modified and that functions to isolate one chemicalprocess (e.g., a binding event; an incorporation reaction; addition orremoval of a protecting moiety, addition or removal of a blocking moietysuch as a reversible terminator) from another, or to provide a space inwhich a chemical process can take place.

As used herein, the terms “degrade” and “degradation”, when referring toa nucleotide, or a portion of the nucleotide, mean chemical modificationof the nucleotide, or a portion of the nucleotide, resulting in adifferent molecule having at least one modulated function or activityrelative to the original (i.e., undegraded) nucleotide, or portion ofthe nucleotide. In some embodiments the terms “degrade” and“degradation”, when referring to a nucleobase, mean chemicalmodification of the nucleobase resulting in a modulated activity orfunction of the nucleobase or the nucleotide or nucleoside including thenucleobase. In embodiments, degradation of a nucleobase may be referredto as “nucleotide degradation”. In embodiments degradation of a specifictype of nucleobase or nucleotide may be referred to as degradation ofthe specific nucleobase type or nucleotide type, for example “dCdegradation” refers to degradation of a deoxycytidine (e.g., degradationof a cytosine nucleobase in a deoxycytidine, degradation of adeoxycytidine in a deoxycytidine triphosphate, degradation of a cytosinenucleobase in an DNA nucleic acid). FIG. 3 depicts an example of areaction resulting in a degraded dC.

The embodiments set forth below and recited in the claims can beunderstood in view of the above definitions.

Compositions and Methods

The present disclosure provides compositions that comprise a solutioncontaining a nucleotide having a protecting group such as a 3′-O-oximemoiety and a reagent having the structure R2 tethered to a reversibleterminator such as R2-ONH₂, wherein R2 is —C(R6)(R7)(R8), —C(O)(R6),—P(O)(R6)(R7), —C(R6)(═C(R7)(R8)), —Si(R6)(R7)(R8), —S O₂(R6),substituted or unsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C5-C6),substituted or unsubstituted cycloalkenyl (e.g., C₃-C₈, C₃-C₆, orC₅-C₆), substituted or unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆,or C₅-C₆), substituted or unsubstituted heteroalicyclyl (e.g., 3 to 8membered, 3 to 6 membered, or 5 to 6 membered), substituted orunsubstituted aryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl), orsubstituted or unsubstituted heteroaryl (e.g., 5 to 10 memberedheteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl).In embodiments, R2 has a molecular weight greater than methyl. Inembodiments, R2 has a molecular weight greater than ethyl. Inembodiments, R2 has a molecular weight greater than 36 g/mol. Inembodiments, R2 has a molecular weight greater than 57 g/mol. Inembodiments, R2 has a molecular weight greater than 100 g/mol. Inembodiments, R2 has a molecular weight greater than 200 g/mol. Inembodiments, R2 has a molecular weight greater than 300 g/mol. Inembodiments, R2 has a molecular weight greater than 400 g/mol. Inembodiments, R2 has a molecular weight greater than 500 g/mol. Inembodiments, R2 has a molecular weight greater than 600 g/mol. Inembodiments, R2 has a molecular weight greater than 700 g/mol. Inembodiments, R2 has a molecular weight greater than 800 g/mol. Inembodiments, R2 has a molecular weight greater than 900 g/mol. Inembodiments, R2 has a molecular weight less than or equal to 1000 g/mol.In embodiments, R2 has a molecular weight less than 1000 g/mol. Althoughnot wishing to be limited by mechanism, it is believed that R2 moietieshaving more steric bulk than hydrogen and methyl yield improvedsynthetic results compared to smaller moieties, and produce fewerunwanted modifications to nucleic acids and nucleotides. See the resultsof Example 1A below. In embodiments, R2 is —C(R6)(R7)(R8) and R6, R7,and R8 are not all hydrogen. Similarly, in some cases R2 isindependently alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl,cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl,(heteroalicyclyl)alkyl, or an optionally substituted variant thereof. Inparticular configurations, the nucleotide has the structure:

B can be a nucleobase. R1 can independently be a halogen, OCH₃, H or OH.Q can be independently monophosphate, diphosphate, triphosphate,hydrogen, or nucleic acid. R3 and R4 can be independently H, CH₃, alkyl,alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl,heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl,(heteroalicyclyl)alkyl, or an optionally substituted variant thereof, oran exogenous label moiety. In embodiments, R3 and R4 can beindependently H, CH₃, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl,cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl,(heteroalicyclyl)alkyl, or an optionally substituted variant thereof. Byway of example, the moiety at the 3′ position of the nucleotide can bean aldoxime (i.e. one of R3 or R4 is hydrogen) or a ketoxime (neither ofR3 or R4 is hydrogen).

Substituted and unsubstituted B moieties are both consistent with thedisclosure herein. In embodiments, B is substituted. In embodiments, Bis unsubstituted. In embodiments, a substituted B (e.g., a substitutednucleobase) is substituted with at least one substituent group,size-limited substituent group, or lower substituent group; wherein ifthe substituted B is substituted with a plurality of groups selectedfrom substituent groups, size-limited substituent groups, and lowersubstituent groups; each substituent group, size-limited substituentgroup, and/or lower substituent group may optionally be different. Inembodiments, when B is substituted, it is substituted with at least onesubstituent group. In embodiments, when B is substituted, it issubstituted with at least one size-limited substituent group. Inembodiments, when B is substituted, it is substituted with at least onelower substituent group. In embodiments, B is a substituted adeninemoiety. In embodiments, B is a substituted cytosine moiety. Inembodiments, B is a substituted guanine moiety. In embodiments, B is asubstituted thymine moiety. In embodiments, B is a substituted uracilmoiety. In embodiments, B is an unsubstituted adenine moiety. Inembodiments, B is an unsubstituted cytosine moiety. In embodiments, B isan unsubstituted guanine moiety. In embodiments, B is an unsubstitutedthymine moiety. In embodiments, B is an unsubstituted uracil moiety.

Similarly, substituted and unsubstituted Q moieties are consistent withthe disclosure herein. In embodiments, Q is substituted. In embodiments,Q is unsubstituted. In embodiments, a substituted Q (e.g., a substitutedmonophosphate, substituted diphosphate, substituted triphosphate,hydrogen atom, and/or substituted nucleic acid) is substituted with atleast one substituent group, size-limited substituent group, or lowersubstituent group; wherein if the substituted Q is substituted with aplurality of groups selected from substituent groups, size-limitedsubstituent groups, and lower substituent groups; each substituentgroup, size-limited substituent group, and/or lower substituent groupmay optionally be different. In embodiments, when Q is substituted, itis substituted with at least one substituent group. In embodiments, whenQ is substituted, it is substituted with at least one size-limitedsubstituent group. In embodiments, when Q is substituted, it issubstituted with at least one lower substituent group.

In embodiments, Q is deoxyribonucleic acid. In embodiments, Q isribonucleic acid. In embodiments, Q is independently monophosphate,diphosphate, triphosphate, or nucleic acid.

In embodiments, R1 is H. In embodiments, R1 is OH.

In embodiments, a substituted R3 (e.g., substituted alkyl, substitutedalkenyl, substituted alkynyl, substituted cycloalkyl, substitutedcycloalkenyl, substituted cycloalkynyl, substituted aryl, substitutedheteroaryl, substituted heteroalicyclyl, substituted aralkyl,substituted heteroaralkyl, and/or substituted (heteroalicyclyl)alkyl) issubstituted with at least one substituent group, size-limitedsubstituent group, or lower substituent group; wherein if thesubstituted R3 is substituted with a plurality of groups selected fromsubstituent groups, size-limited substituent groups, and lowersubstituent groups; each substituent group, size-limited substituentgroup, and/or lower substituent group may optionally be different. Inembodiments, when R3 is substituted, it is substituted with at least onesubstituent group. In embodiments, when R3 is substituted, it issubstituted with at least one size-limited substituent group. Inembodiments, when R3 is substituted, it is substituted with at least onelower substituent group.

In embodiments, R3 is independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof, or an exogenous label moiety. Inembodiments, R3 is independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof. In embodiments, R3 isindependently an exogenous label moiety.

In embodiments, a substituted R4 (e.g., substituted alkyl, substitutedalkenyl, substituted alkynyl, substituted cycloalkyl, substitutedcycloalkenyl, substituted cycloalkynyl, substituted aryl, substitutedheteroaryl, substituted heteroalicyclyl, substituted aralkyl,substituted heteroaralkyl, and/or substituted (heteroalicyclyl)alkyl) issubstituted with at least one substituent group, size-limitedsubstituent group, or lower substituent group; wherein if thesubstituted R4 is substituted with a plurality of groups selected fromsubstituent groups, size-limited substituent groups, and lowersubstituent groups; each substituent group, size-limited substituentgroup, and/or lower substituent group may optionally be different. Inembodiments, when R4 is substituted, it is substituted with at least onesubstituent group. In embodiments, when R4 is substituted, it issubstituted with at least one size-limited substituent group. Inembodiments, when R4 is substituted, it is substituted with at least onelower substituent group.

In embodiments, R4 is independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof, or an exogenous label moiety. Inembodiments, R4 is independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof. In embodiments, R4 isindependently an exogenous label moiety.

In embodiments, the solution is an aqueous solution. In embodiments, thenucleotide is attached to a solid support and wherein the solid supportis in contact with the solution. In embodiments, the reagent thatcomprises the structure R2-ONH₂ is attached to a solid support incontact with the aqueous solution. In embodiments, the nucleobasecomprises an exogenous label moiety.

The present disclosure also provides methods for modifying a nucleotide.The methods can be carried out by reacting a nucleotide having aprotecting moiety such as a 3′-O-oxime moiety to a reagent having thestructure R2-block, wherein block is a blocking moiety such as thereversible terminator moiety —ONH₂, to produce a nucleotide having a3′-O—NH₂ moiety or other moiety as a blocking moiety or a reversibleterminator. In some cases R2 is independently alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof. R2 can be an alkyl other thanmethyl. In embodiments, R2 is not —CH₃. In embodiments, R2 is nothydrogen. In embodiments, R2 is not hydrogen, or —CH₃. The presentdisclosure also provides a method for modifying a nucleotide. The methodcan be carried out by reacting a nucleotide having a 3′-O-oxime moietywith a reagent having the structure R2-ONH₂ to produce a nucleotidehaving a 3′-O—NH₂ moiety, wherein R2 is independently alkyl, alkenyl,alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

In embodiments, a substituted R2 (e.g., substituted alkyl, substitutedalkenyl, substituted alkynyl, substituted cycloalkyl, substitutedcycloalkenyl, substituted cycloalkynyl, substituted aryl, substitutedheteroaryl, substituted heteroalicyclyl, substituted aralkyl,substituted heteroaralkyl, and/or substituted (heteroalicyclyl)alkyl) issubstituted with at least one substituent group, size-limitedsubstituent group, or lower substituent group; wherein if thesubstituted R2 is substituted with a plurality of groups selected fromsubstituent groups, size-limited substituent groups, and lowersubstituent groups; each substituent group, size-limited substituentgroup, and/or lower substituent group may optionally be different. Inembodiments, when R2 is substituted, it is substituted with at least onesubstituent group. In embodiments, when R2 is substituted, it issubstituted with at least one size-limited substituent group. Inembodiments, when R2 is substituted, it is substituted with at least onelower substituent group.

In embodiments, R2 is —C(R6)(R7)(R8), —C(O)(R6), —P(O)(R6)(R7),—C(R6)(═C(R7)(R8)), —Si(R6)(R7)(R8), —S O₂(R6), substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C5-C6), substituted orunsubstituted cycloalkenyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆), substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆),substituted or unsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3to 6 membered, or 5 to 6 membered), substituted or unsubstituted aryl(e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl), or substituted orunsubstituted heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9membered heteroaryl, or 5 to 6 membered heteroaryl).

In embodiments, R2 is —C(R6)(R7)(R8). In embodiments, R2 is —C(O)(R6).In embodiments, R2 is —P(O)(R6)(R7). In embodiments, R2 is—C(R6)(═C(R7)(R8)). In embodiments, R2 is —Si(R6)(R7)(R8). Inembodiments, R2 is —SO₂(R6). In embodiments, R2 is substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments,R2 is substituted or unsubstituted cycloalkenyl (e.g., C₃-C₈, C₃-C₆, orC₅-C₆). In embodiments, R2 is substituted or unsubstituted cycloalkynyl(e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R2 is substituted orunsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered,or 5 to 6 membered). In embodiments, R2 is substituted or unsubstitutedaryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). In embodiments, R2 issubstituted or unsubstituted heteroaryl (e.g., 5 to 10 memberedheteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl).In embodiments, R2 is unsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, orC₅-C₆). In embodiments, R2 is unsubstituted cycloalkenyl (e.g., C₃-C₈,C₃-C₆, or C₅-C₆). In embodiments, R2 is unsubstituted cycloalkynyl(e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R2 is unsubstitutedheteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered, or 5 to 6membered). In embodiments, R2 is unsubstituted aryl (e.g., C₆-C₁₀ aryl,C₁₀ aryl, or phenyl). In embodiments, R2 is unsubstituted heteroaryl(e.g., 5 to 10 membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to6 membered heteroaryl). In embodiments, R2 is not unsubstituted methyl.In embodiments, R2 is not unsubstituted ethyl. In embodiments, R2 is notunsubstituted propyl.

R6, R7, and R8 are independently hydrogen, halogen, —CCl₃, —CBr₃, —CF₃,—CI₃, —CHCl₂, —CHBr₂, —CHF₂, —CHI₂, —CH₂Cl, —CH₂Br, —CH₂F, —CH₂I, —CN,—OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂,—ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂, —NHSO₂H, —NHC(O)H, —NHC(O)OH, —NHOH,—OCCl₃, —OCF₃, —OCBr₃, —OCI₃, —OCHCl₂, —OCHBr₂, —OCHI₂, —OCHF₂, —OCH₂Cl,—OCH₂Br, —OCH₂I, —OCH₂F, —SF₅, —N₃, substituted or unsubstituted alkyl(e.g., C₁-C₈ alkyl, C₁-C₆ alkyl, or C1-C4 alkyl), substituted orunsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆ alkenyl, or C2-C4alkenyl), substituted or unsubstituted alkynyl (e.g., C₂-C₈ alkynyl,C₂-C₆ alkynyl, or C₂-C₄ alkynyl), substituted or unsubstitutedheteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to 6 memberedheteroalkyl, or 2 to 4 membered heteroalkyl), substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆), substituted orunsubstituted cycloalkenyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆), substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆),substituted or unsubstituted aryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, orphenyl), substituted or unsubstituted heteroaryl (e.g., 5 to 10 memberedheteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl),substituted or unsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3to 6 membered, or 5 to 6 membered), substituted or unsubstitutedaralkyl, substituted or unsubstituted heteroaralkyl, substituted orunsubstituted (heteroalicyclyl)alkyl, or an exogenous label moiety. Inembodiments, R6, R7, and R8 are not all hydrogen. In embodiments, R6 isnot hydrogen. In embodiments, R7 is not hydrogen. In embodiments, R8 isnot hydrogen. In embodiments, R2 is —C(R6)(R7)(R8) and R6, R7, and R8are not all hydrogen.

In embodiments, R6, R7, and R8 are independently hydrogen, halogen,—CCl₃, —CBr₃, —CF₃, —CI₃, —CHCl₂, —CHBr₂, —CHF₂, —CHI₂, —CH₂Cl, —CH₂Br,—CH₂F, —CH₂I, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₃H, —SO₄H,—SO₂NH₂, —NHNH₂, —ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂, —NHSO₂H, —NHC(O)H,—NHC(O)OH, —NHOH, —OCCl₃, —OCF₃, —OCBr₃, —OCI₃, —OCHCl₂, —OCHBr₂,—OCHI₂, —OCHF₂, —OCH₂Cl, —OCH₂Br, —OCH₂I, —OCH₂F, —SF₅, —N₃, substitutedor unsubstituted alkyl (e.g., C₁-C₈ alkyl, C₁-C₆ alkyl, or C₁-C₄ alkyl),substituted or unsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆alkenyl, or C2-C4 alkenyl), substituted or unsubstituted alkynyl (e.g.,C₂-C₈ alkynyl, C₂-C₆ alkynyl, or C₂-C₄ alkynyl), substituted orunsubstituted heteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to 6membered heteroalkyl, or 2 to 4 membered heteroalkyl), substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆), substituted orunsubstituted cycloalkenyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆), substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆),substituted or unsubstituted aryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, orphenyl), substituted or unsubstituted heteroaryl (e.g., 5 to 10 memberedheteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl),substituted or unsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3to 6 membered, or 5 to 6 membered), substituted or unsubstitutedaralkyl, substituted or unsubstituted heteroaralkyl, or substituted orunsubstituted (heteroalicyclyl)alkyl. In embodiments, R6, R7, and R8 arenot all hydrogen. In embodiments, R6 is not hydrogen. In embodiments, R7is not hydrogen. In embodiments, R8 is not hydrogen. In embodiments, R2is —C(R6)(R7)(R8) and R6, R7, and R8 are not all hydrogen.

In embodiments, a substituted R6 (e.g., substituted alkyl, substitutedalkenyl, substituted alkynyl, substituted heteroalkyl, substitutedcycloalkyl, substituted cycloalkenyl, substituted cycloalkynyl,substituted aryl, substituted heteroaryl, substituted heteroalicyclyl,substituted aralkyl, substituted heteroaralkyl, and/or substituted(heteroalicyclyl)alkyl) is substituted with at least one substituentgroup, size-limited substituent group, or lower substituent group;wherein if the substituted R6 is substituted with a plurality of groupsselected from substituent groups, size-limited substituent groups, andlower substituent groups; each substituent group, size-limitedsubstituent group, and/or lower substituent group may optionally bedifferent. In embodiments, when R6 is substituted, it is substitutedwith at least one substituent group. In embodiments, when R6 issubstituted, it is substituted with at least one size-limitedsubstituent group. In embodiments, when R6 is substituted, it issubstituted with at least one lower substituent group.

In embodiments, R6 is independently hydrogen. In embodiments, R6 isindependently halogen. In embodiments, R6 is independently —CCl₃. Inembodiments, R6 is independently —CBr₃. In embodiments, R6 isindependently —CF₃. In embodiments, R6 is independently —CI₃. Inembodiments, R6 is independently —CHCl₂. In embodiments, R6 isindependently —CHBr₂. In embodiments, R6 is independently —CHF₂. Inembodiments, R6 is independently —CHI₂. In embodiments, R6 isindependently —CH₂Cl. In embodiments, R6 is independently —CH₂Br. Inembodiments, R6 is independently —CH₂F. In embodiments, R6 isindependently —CH₂I. In embodiments, R6 is independently —CN. Inembodiments, R6 is independently —OH. In embodiments, R6 isindependently —NH₂. In embodiments, R6 is independently —COOH. Inembodiments, R6 is independently —CONH₂. In embodiments, R6 isindependently —NO₂. In embodiments, R6 is independently —SH. Inembodiments, R6 is independently —SO₃H. In embodiments, R6 isindependently —SO₄H. In embodiments, R6 is independently —SO₂NH₂. Inembodiments, R6 is independently —NHNH₂. In embodiments, R6 isindependently —ONH₂. In embodiments, R6 is independently —NHC(O)NHNH₂.In embodiments, R6 is independently —NHC(O)NH₂. In embodiments, R6 isindependently —NHSO₂H. In embodiments, R6 is independently —NHC(O)H. Inembodiments, R6 is independently —NHC(O)OH. In embodiments, R6 isindependently —NHOH. In embodiments, R6 is independently —OCCl₃. Inembodiments, R6 is independently —OCF₃. In embodiments, R6 isindependently —OCBr₃. In embodiments, R6 is independently —OCI₃. Inembodiments, R6 is independently —OCHCl₂. In embodiments, R6 isindependently —OCHBr₂. In embodiments, R6 is independently —OCHI₂. Inembodiments, R6 is independently —OCHF₂. In embodiments, R6 isindependently —OCH₂Cl. In embodiments, R6 is independently —OCH₂Br. Inembodiments, R6 is independently —OCH₂I. In embodiments, R6 isindependently —OCH₂F. In embodiments, R6 is independently —SF₅. Inembodiments, R6 is independently —N₃. In embodiments, R6 isindependently substituted or unsubstituted alkyl (e.g., C₁-C₈ alkyl,C₁-C₆ alkyl, or C₁-C₄ alkyl). In embodiments, R6 is independentlysubstituted or unsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆alkenyl, or C₂-C₄ alkenyl). In embodiments, R6 is independentlysubstituted or unsubstituted alkynyl (e.g., C₂-C₈ alkynyl, C₂-C₆alkynyl, or C2-C4 alkynyl). In embodiments, R6 is independentlysubstituted or unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R6 is independently substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments,R6 is independently substituted or unsubstituted cycloalkenyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R6 is independently substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). Inembodiments, R6 is independently substituted or unsubstituted aryl(e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). In embodiments, R6 isindependently substituted or unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R6 is independently substituted orunsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered,or 5 to 6 membered). In embodiments, R6 is independently substituted orunsubstituted aralkyl. In embodiments, R6 is independently substitutedor unsubstituted heteroaralkyl. In embodiments, R6 is independentlysubstituted or unsubstituted (heteroalicyclyl)alkyl. In embodiments, R6is independently an exogenous label moiety.

In embodiments, R6 is independently unsubstituted alkyl (e.g., C₁-C₈alkyl, C₁-C₆ alkyl, or C₁-C₄ alkyl). In embodiments, R6 is independentlyunsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆ alkenyl, or C₂-C₄alkenyl). In embodiments, R6 is independently unsubstituted alkynyl(e.g., C₂-C₈ alkynyl, C₂-C₆ alkynyl, or C2-C4 alkynyl). In embodiments,R6 is independently unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R6 is independently unsubstitutedcycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R6 isindependently unsubstituted cycloalkenyl (e.g., C₃-C₈, C3-C6, or C₅-C₆).In embodiments, R6 is independently unsubstituted cycloalkynyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R6 is independentlyunsubstituted aryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). Inembodiments, R6 is independently unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R6 is independently unsubstitutedheteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered, or 5 to 6membered). In embodiments, R6 is independently unsubstituted aralkyl. Inembodiments, R6 is independently unsubstituted heteroaralkyl. Inembodiments, R6 is independently unsubstituted (heteroalicyclyl)alkyl.

In embodiments, a substituted R7 (e.g., substituted alkyl, substitutedalkenyl, substituted alkynyl, substituted heteroalkyl, substitutedcycloalkyl, substituted cycloalkenyl, substituted cycloalkynyl,substituted aryl, substituted heteroaryl, substituted heteroalicyclyl,substituted aralkyl, substituted heteroaralkyl, and/or substituted(heteroalicyclyl)alkyl) is substituted with at least one substituentgroup, size-limited substituent group, or lower substituent group;wherein if the substituted R7 is substituted with a plurality of groupsselected from substituent groups, size-limited substituent groups, andlower substituent groups; each substituent group, size-limitedsubstituent group, and/or lower substituent group may optionally bedifferent. In embodiments, when R7 is substituted, it is substitutedwith at least one substituent group. In embodiments, when R7 issubstituted, it is substituted with at least one size-limitedsubstituent group. In embodiments, when R7 is substituted, it issubstituted with at least one lower substituent group.

In embodiments, R7 is independently hydrogen. In embodiments, R7 isindependently halogen. In embodiments, R7 is independently —CCl₃. Inembodiments, R7 is independently —CBr₃. In embodiments, R7 isindependently —CF₃. In embodiments, R7 is independently —CI₃. Inembodiments, R7 is independently —CHCl₂. In embodiments, R7 isindependently —CHBr₂. In embodiments, R7 is independently —CHF₂. Inembodiments, R7 is independently —CHI₂. In embodiments, R7 isindependently —CH₂Cl. In embodiments, R7 is independently —CH₂Br. Inembodiments, R7 is independently —CH₂F. In embodiments, R7 isindependently —CH₂I. In embodiments, R7 is independently —CN. Inembodiments, R7 is independently —OH. In embodiments, R7 isindependently —NH₂. In embodiments, R7 is independently —COOH. Inembodiments, R7 is independently —CONH₂. In embodiments, R7 isindependently —NO₂. In embodiments, R7 is independently —SH. Inembodiments, R7 is independently —SO₃H. In embodiments, R7 isindependently —SO₄H. In embodiments, R7 is independently —SO₂NH₂. Inembodiments, R7 is independently —NHNH₂. In embodiments, R7 isindependently —ONH₂. In embodiments, R7 is independently —NHC(O)NHNH₂.In embodiments, R7 is independently —NHC(O)NH₂. In embodiments, R7 isindependently —NHSO₂H. In embodiments, R7 is independently —NHC(O)H. Inembodiments, R7 is independently —NHC(O)OH. In embodiments, R7 isindependently —NHOH. In embodiments, R7 is independently —OCCl₃. Inembodiments, R7 is independently —OCF₃. In embodiments, R7 isindependently —OCBr₃. In embodiments, R7 is independently —OCI₃. Inembodiments, R7 is independently —OCHCl₂. In embodiments, R7 isindependently —OCHBr₂. In embodiments, R7 is independently —OCHI₂. Inembodiments, R7 is independently —OCHF₂. In embodiments, R7 isindependently —OCH₂Cl. In embodiments, R7 is independently —OCH₂Br. Inembodiments, R7 is independently —OCH₂I. In embodiments, R7 isindependently —OCH₂F. In embodiments, R7 is independently —SF₅. Inembodiments, R7 is independently —N₃. In embodiments, R7 isindependently substituted or unsubstituted alkyl (e.g., C₁-C₈ alkyl,C₁-C₆ alkyl, or C1-C4 alkyl). In embodiments, R7 is independentlysubstituted or unsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆alkenyl, or C₂-C₄ alkenyl). In embodiments, R7 is independentlysubstituted or unsubstituted alkynyl (e.g., C₂-C₈ alkynyl, C₂-C₆alkynyl, or C2-C4 alkynyl). In embodiments, R7 is independentlysubstituted or unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R7 is independently substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments,R7 is independently substituted or unsubstituted cycloalkenyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R7 is independently substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). Inembodiments, R7 is independently substituted or unsubstituted aryl(e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). In embodiments, R7 isindependently substituted or unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R7 is independently substituted orunsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered,or 5 to 6 membered). In embodiments, R7 is independently substituted orunsubstituted aralkyl. In embodiments, R7 is independently substitutedor unsubstituted heteroaralkyl. In embodiments, R7 is independentlysubstituted or unsubstituted (heteroalicyclyl)alkyl. In embodiments, R7is independently an exogenous label moiety.

In embodiments, R7 is independently unsubstituted alkyl (e.g., C₁-C₈alkyl, C₁-C₆ alkyl, or C₁-C₄ alkyl). In embodiments, R7 is independentlyunsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆ alkenyl, or C₂-C₄alkenyl). In embodiments, R7 is independently unsubstituted alkynyl(e.g., C₂-C₈ alkynyl, C₂-C₆ alkynyl, or C2-C4 alkynyl). In embodiments,R7 is independently unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R7 is independently unsubstitutedcycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R7 isindependently unsubstituted cycloalkenyl (e.g., C₃-C₈, C3-C6, or C₅-C₆).In embodiments, R7 is independently unsubstituted cycloalkynyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R7 is independentlyunsubstituted aryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). Inembodiments, R7 is independently unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R7 is independently unsubstitutedheteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered, or 5 to 6membered). In embodiments, R7 is independently unsubstituted aralkyl. Inembodiments, R7 is independently unsubstituted heteroaralkyl. Inembodiments, R7 is independently unsubstituted (heteroalicyclyl)alkyl.

In embodiments, a substituted R8 (e.g., substituted alkyl, substitutedalkenyl, substituted alkynyl, substituted heteroalkyl, substitutedcycloalkyl, substituted cycloalkenyl, substituted cycloalkynyl,substituted aryl, substituted heteroaryl, substituted heteroalicyclyl,substituted aralkyl, substituted heteroaralkyl, and/or substituted(heteroalicyclyl)alkyl) is substituted with at least one substituentgroup, size-limited substituent group, or lower substituent group;wherein if the substituted R8 is substituted with a plurality of groupsselected from substituent groups, size-limited substituent groups, andlower substituent groups; each substituent group, size-limitedsubstituent group, and/or lower substituent group may optionally bedifferent. In embodiments, when R8 is substituted, it is substitutedwith at least one substituent group. In embodiments, when R8 issubstituted, it is substituted with at least one size-limitedsubstituent group. In embodiments, when R8 is substituted, it issubstituted with at least one lower substituent group.

In embodiments, R8 is independently hydrogen. In embodiments, R8 isindependently halogen. In embodiments, R8 is independently —CCl₃. Inembodiments, R8 is independently —CBr₃. In embodiments, R8 isindependently —CF₃. In embodiments, R8 is independently —CI₃. Inembodiments, R8 is independently —CHCl₂. In embodiments, R8 isindependently —CHBr₂. In embodiments, R8 is independently —CHF₂. Inembodiments, R8 is independently —CHI₂. In embodiments, R8 isindependently —CH₂Cl. In embodiments, R8 is independently —CH₂Br. Inembodiments, R8 is independently —CH₂F. In embodiments, R8 isindependently —CH₂I. In embodiments, R8 is independently —CN. Inembodiments, R8 is independently —OH. In embodiments, R8 isindependently —NH₂. In embodiments, R8 is independently —COOH. Inembodiments, R8 is independently —CONH₂. In embodiments, R8 isindependently —NO₂. In embodiments, R8 is independently —SH. Inembodiments, R8 is independently —SO₃H. In embodiments, R8 isindependently —SO₄H. In embodiments, R8 is independently —SO₂NH₂. Inembodiments, R8 is independently —NHNH₂. In embodiments, R8 isindependently —ONH₂. In embodiments, R8 is independently —NHC(O)NHNH₂.In embodiments, R8 is independently —NHC(O)NH₂. In embodiments, R8 isindependently —NHSO₂H. In embodiments, R8 is independently —NHC(O)H. Inembodiments, R8 is independently —NHC(O)OH. In embodiments, R8 isindependently —NHOH. In embodiments, R8 is independently —OCCl₃. Inembodiments, R8 is independently —OCF₃. In embodiments, R8 isindependently —OCBr₃. In embodiments, R8 is independently —OCI₃. Inembodiments, R8 is independently —OCHCl₂. In embodiments, R8 isindependently —OCHBr₂. In embodiments, R8 is independently —OCHI₂. Inembodiments, R8 is independently —OCHF₂. In embodiments, R8 isindependently —OCH₂Cl. In embodiments, R8 is independently —OCH₂Br. Inembodiments, R8 is independently —OCH₂I. In embodiments, R8 isindependently —OCH₂F. In embodiments, R8 is independently —SF₅. Inembodiments, R8 is independently —N₃. In embodiments, R8 isindependently substituted or unsubstituted alkyl (e.g., C₁-C₈ alkyl,C₁-C₆ alkyl, or C₁-C₄ alkyl). In embodiments, R8 is independentlysubstituted or unsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆alkenyl, or C₂-C₄ alkenyl). In embodiments, R8 is independentlysubstituted or unsubstituted alkynyl (e.g., C₂-C₈ alkynyl, C₂-C₆alkynyl, or C2-C4 alkynyl). In embodiments, R8 is independentlysubstituted or unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R8 is independently substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments,R8 is independently substituted or unsubstituted cycloalkenyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R8 is independently substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). Inembodiments, R8 is independently substituted or unsubstituted aryl(e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). In embodiments, R8 isindependently substituted or unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R8 is independently substituted orunsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered,or 5 to 6 membered). In embodiments, R8 is independently substituted orunsubstituted aralkyl. In embodiments, R8 is independently substitutedor unsubstituted heteroaralkyl. In embodiments, R8 is independentlysubstituted or unsubstituted (heteroalicyclyl)alkyl. In embodiments, R8is independently an exogenous label moiety.

In embodiments, R8 is independently unsubstituted alkyl (e.g., C₁-C₈alkyl, C₁-C₆ alkyl, or C₁-C₄ alkyl). In embodiments, R8 is independentlyunsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆ alkenyl, or C₂-C₄alkenyl). In embodiments, R8 is independently unsubstituted alkynyl(e.g., C₂-C₈ alkynyl, C₂-C₆ alkynyl, or C2-C4 alkynyl). In embodiments,R8 is independently unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R8 is independently unsubstitutedcycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R8 isindependently unsubstituted cycloalkenyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆).In embodiments, R8 is independently unsubstituted cycloalkynyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R8 is independentlyunsubstituted aryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). Inembodiments, R8 is independently unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R8 is independently unsubstitutedheteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered, or 5 to 6membered). In embodiments, R8 is independently unsubstituted aralkyl. Inembodiments, R8 is independently unsubstituted heteroaralkyl. Inembodiments, R8 is independently unsubstituted (heteroalicyclyl)alkyl.

Turning to FIG. 1A, one sees that with increasing R2 size, one observesa decreasing percentage of dC degradation in final reaction product asobserved after 60 minutes of a 25 C reaction. One also observes that R2moieties having at least two carbon atoms perform better in terms ofstarting material consumption than do smaller R2 moieties.

In some configurations, the nucleotide that has the 3′-O-oxime moietycan have the structure:

and the nucleotide that has the 3′-O—NH₂ moiety can have the structure:

B can be a nucleobase. R1 can independently be a halogen, OCH₃, H or OH.Q can be independently monophosphate, diphosphate, triphosphate, ornucleic acid. R3 and R4 can be independently H, CH₃, alkyl, alkenyl,alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof. By way of example, the moiety atthe 3′ position of the nucleotide can be an aldoxime (i.e. one of R3 orR4 is hydrogen) or a ketoxime (neither of R3 or R4 is hydrogen).

In embodiments, the reaction occurs in an aqueous solution. Inembodiments, the nucleotide is attached to a solid support in contactwith the aqueous solution.

In embodiments, the nucleotide that is produced comprises adeoxynucleotide. In embodiments, the nucleotide that is producedincludes:

wherein Base is the nucleobase, and wherein DNA is independently asingle stranded deoxyribonucleic acid or double strandeddeoxyribonucleic acid. In embodiments, Base has a value of B.

In embodiments, the reagent is independently one of:

Additional individual examples of the reagent include the moleculeslisted in FIG. 1B and the molecules listed in FIG. 2. The presentdisclosure also provides a method for modifying a nucleotide. The methodcan be carried out by reacting a nucleotide having a 3′-O-oxime moietywith a reagent having the structure R2-ONH₂ to produce a nucleotidehaving a 3′-O—NH₂ moiety, wherein R2 is independently alkyl, alkenyl,alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof. In some configurations, thenucleotide that has the 3′-O-oxime moiety can have the structure:

and the nucleotide that has the 3′-O—NH₂ moiety can have the structure:

B can be a nucleobase. R1 can independently be a halogen, OCH₃, H or OH.Q can be independently monophosphate, diphosphate, triphosphate, ornucleic acid. R3 and R4 can be independently H, CH₃, alkyl, alkenyl,alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof. By way of example, the moiety atthe 3′ position of the nucleotide can be an aldoxime (i.e. one of R3 orR4 is hydrogen) or a ketoxime (neither of R3 or R4 is hydrogen).

A method or composition of the present disclosure can include any of avariety of nucleotides. The nucleotide can be a native nucleotide,nucleotide analog or modified nucleotide as desired to suit a particularapplication or configuration set forth herein. Optionally, a nucleotidehas a nitrogenous base, five-carbon sugar, and phosphate group, whereinany moiety of the nucleotide may be modified, removed and/or replaced ascompared to a native nucleotide. For example, the 5′ oxygen of anucleotide need not have a phosphate moiety and can instead be protectedwith an exogenous moiety such as dimethoxytrityl (DMT) moiety. Reactiveatoms in the base moiety of a nucleotide can be protected with exogenousmoieties if desired. Often, methods and compositions disclosed hereincomprise cytosine bases, and the cytosine bases are preserved in anundegraded or unmodified form at a higher rate than comparable methodsor compositions in the prior art, as represented for example by thepoint DRT 1 in FIG. 1A.

Nucleotides that are used in a composition, method, apparatus or systemherein can include terminators that reversibly prevent subsequentnucleotide incorporation at the 3′-end of the primer after the analoghas been incorporated into the primer. For example, U.S. Pat. No.7,544,794 (published Jun. 9, 2009), U.S. Pat. No. 8,034,923 (publishedOct. 11, 2011) and U.S. Pat. No. 10,472,383 (published Nov. 12, 2019)(the disclosures of each of which being incorporated herein by referencein their respective entireties) describe reversible terminators in whichthe 3′-OH group is replaced by a 3′-ONH₂ moiety. These reversibleterminators are resistant to modification by nucleic acid enzymes suchas polymerases and ligases such that they prevent addition of asubsequent base at the 3′ blocked position, thereby terminatingextension of the nucleic acid strand when they are incorporated. Theamino moiety can be removed from a nucleotide (for example, when thenucleotide is at the 3′ end of a primer) by nitrous acid (HONO), therebydeblocking the nucleotide. The deblocked nucleotide will have a 3′OHthat can be acted upon by a polymerase such that the 3′ oxygen forms acovalent bond with the 5′ phosphate of another nucleotide in a reactionknown as an incorporation reaction or extension reaction. Removal of theamino moiety from a nucleotide via a deblocking step can similarly allowthe nucleotide to be acted upon by a ligase such that the 3′ oxygenforms a covalent bond with the 5′ phosphate of an oligonucleotide in anincorporation or extension reaction.

A number of blocking moieties are consistent with the disclosure herein.Some blocking moieties share the characteristic that they do notprohibit the nucleotide to which they are bound from being incorporatedat their 5′ ends to an available 3′ OH moiety by a nucleotidepolymerizing enzyme, so as to incorporate the nucleotide that blocksfurther extension. Generally, larger moieties such as protectingmoieties are often too large to be incorporated by nucleic acidpolymerase enzyme. In embodiments, 3′-reversible terminators and 3′blocking moieties include —ONH₂, —ONHCH₃, —OCH₂N₃, and —ONHCOCH₃. Inembodiments, a 3′-blocking moiety is —ONH₂. In embodiments, a3′-blocking moiety is —ONHCH₃. In embodiments, a 3′-blocking moiety is—OCH₂N₃. In embodiments, a 3′-blocking moiety is and —ONHCOCH₃. Inembodiments, a 3′-blocking moiety is a 3′-O-oxime moiety. Inembodiments, a 3′-reversible terminator moiety is a 3′-O-oxime moiety.

The present disclosure provides new and useful reagents and methods forsynthesizing reversibly terminated nucleotides, such as those that havea 3′-ONH₂ moiety. Such reversibly terminated nucleotides can besynthesized by reacting a precursor nucleotide, having a 3′-O-oximemoiety, with an alkoxyamine reagent having the structure R2-ONH₂.Particularly useful reagents include those in which R2 is a moiety otherthan hydrogen. For example, R2 can be alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof. Particularly useful R2 moietiesinclude, for example, —CH₂CH₃, —CH₂CHCH₂, and —C(CH₃)₃. In embodiments,R2 is as described herein, including in embodiments, claims, andfigures. Thus, useful alkoxyamine reagents can include one or more ofthe following molecules:

as well as any of the molecules listed in FIG. 1A or FIG. 2.

Any of a variety of substitutions can be made to the above R2 moieties.For example, one or more of the hydrogens in the —CH₂CH₃ or —CH₂CHCH₂moieties can be substituted with a carbonyl (—CO₂), alcohol (—OH), amine(—NH₂) or halogen (e.g. Bromine, Fluorine, Chlorine, or Iodine).Similarly, one or more of the hydrogens in one or more of the methyls ofthe —C(CH₃)₃ moiety can be substituted in this way. In particular,applications the additional steric bulk provided by these types ofsubstitutions can beneficially favor conversion of a 3′-O-oxime moietyof a nucleotide to a 3′-O—NH₂ moiety over unwanted side reactions thatmodify the nucleobase moiety of the nucleotide.

In embodiments, R2 is independently,

In embodiments, R2 is independently

In embodiments, R2 is independently

In embodiments, R2 is independently

In embodiments, R2 is independently

In embodiments, R2 is independently

In embodiments, R2 is independently

In embodiments, R2 is independently

In embodiments, R2 is independently

In embodiments, R2 is independently

In embodiments, R2 is independently

In embodiments, R2 is independently

In embodiments, R2 is independently

In embodiments, R2 is independently

In embodiments, R2 is independently

In embodiments, R2 is independently

In some configurations of the methods and compositions set forth herein,R2 in the formula R2-ONH₂ can be CH₃. However, R2 need not be CH₃.Rather, R2 can be a higher order alkyl than a methyl (i.e. R2 can havemore than one carbon). Accordingly, R2 can be an alkyl other thanmethyl. In embodiments, R2 is not —CH₃. In embodiments, R2 is nothydrogen. In embodiments, R2 is not hydrogen, or —CH₃. In embodiments,R2 is —C(R6)(R7)(R8), —C(O)(R6), —P(O)(R6)(R7), —C(R6)(═C(R7)(R8)),—Si(R6)(R7)(R8), —S O₂(R6), substituted or unsubstituted cycloalkyl(e.g., C₃-C₈, C₃-C₆, or C5-C6), substituted or unsubstitutedcycloalkenyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆), substituted orunsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆), substitutedor unsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3 to 6membered, or 5 to 6 membered), substituted or unsubstituted aryl (e.g.,C₆-C₁₀ aryl, C₁₀ aryl, or phenyl), or substituted or unsubstitutedheteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9 memberedheteroaryl, or 5 to 6 membered heteroaryl). In embodiments, R2 has amolecular weight greater than methyl. In embodiments, R2 has a molecularweight greater than ethyl. In embodiments, R2 has a molecular weightgreater than 36 g/mol. In embodiments, R2 has a molecular weight greaterthan 57 g/mol. In embodiments, R2 has a molecular weight greater than100 g/mol. In embodiments, R2 has a molecular weight greater than 200g/mol. In embodiments, R2 has a molecular weight greater than 300 g/mol.In embodiments, R2 has a molecular weight greater than 400 g/mol. Inembodiments, R2 has a molecular weight greater than 500 g/mol. Inembodiments, R2 has a molecular weight greater than 600 g/mol. Inembodiments, R2 has a molecular weight greater than 700 g/mol. Inembodiments, R2 has a molecular weight greater than 800 g/mol. Inembodiments, R2 has a molecular weight greater than 900 g/mol. Inembodiments, R2 has a molecular weight less than or equal to 1000 g/mol.In embodiments, R2 has a molecular weight less than 1000 g/mol. Althoughnot wishing to be limited by mechanism, it is believed that R2 moietieshaving more steric bulk than hydrogen and methyl yield improvedsynthetic results compared to smaller moieties, and produce fewerunwanted modifications to nucleic acids and nucleotides. See the resultsof Example 1 below. In embodiments, R2 is —C(R6)(R7)(R8) and R6, R7, andR8 are not all hydrogen. In embodiments, R2 is not unsubstituted methyl.In embodiments, R2 is not unsubstituted ethyl. In embodiments, R2 is notunsubstituted propyl.

Through the disclosure herein, one observes the following. R2 moietiesas disclosed herein perform substantially better than do prior artreagents in driving reactions to near completion. In a 60 minutereaction performed at 25° C., for example, one observes that R2 moietiesas disclosed herein exhibit starting material consumption of at least92%, at least 93%, at least 94%, at least 95%, at least 96%, at least97%, at least 98%, at least 99% or greater than 99% consumption ofnucleotide starting material, whereas prior art approaches achieve lessthan 92%.

Similarly, one observes that with increasing R2 size, one sees adecreasing amount of nucleotide such as dC base degradation, such thatR2 moieties as disclosed herein come to the above-mentioned completionpercentages with no more than 6%, no more than 5%, no more than 4%, nomore than 3%, no more than 2%, no more than 1%, or less than 1%degradation of dC.

Similarly, in some cases one sees a correlation between R2 size andreduction of nucleotide such as dC degradation. Accordingly, disclosedherein are R2 moieties having molecular weights of at least any of thefollowing values: 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36,37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 39, 50, 51, 52, 53, 54,55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72,73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90,91, 92, 93, 94, 95, 96, 97, 98, 99, 100, or greater than 100.

In embodiments, R2 moieties are in some cases limited by solubility,such that in embodiments larger moieties become insoluble. Accordingly,in embodiments, R2 moieties are variously limited to no more than any ofthe following molecular weights: 1000, 900, 800, 700, 650, 600, 550,500, 450, 400, 350, 300, 290, 280, 270, 260, 250, 240, 230, 220, 210,200, 190, 180, 170, 160, 150, 140, 130, 120, 110, 100, or less than 100g/mol.

R2 moieties may comprise a number of constituents, alone or incombination, to covey the benefits disclosed herein. Some R2 moietiesvariously comprise at least 2, at least 3, at least 4, at least 5, atleast 6, or more than 6 carbon nuclei. Similarly, some R2 comprise atleast one of the following: at least 1 nitrogen nucleus, at least onesilicon nucleus, at least one phosphorous nucleus, at least one fluorinenucleus or at least one other constituent. R2 moieties are in some casespartially or fully fluorinated, or partially or fully hydrogenated. Insome cases an R2 moiety comprises at least one component to facilitatesolubility.

Alkoxyamine reagents having the structure R2-ONH₂, wherein R2 is—CH₂CH₃, —CH₂CHCH₂, and —C(CH₃)₃ are soluble in aqueous solution makingthem particularly useful for nucleotide synthesis and modification.Other R2 moieties that provide aqueous solubility can also be used. Insome configurations, synthesis can be carried out using alkoxyaminereagents that are not soluble, or only sparingly soluble, in aqueoussolutions. For example, synthesis can be carried out in non-aqueoussolutions or in liquids formed by mixtures of aqueous and organicsolvents. Exemplary alkoxyamine reagents that can be useful innon-aqueous or partially aqueous liquids include those having phenylmoieties and/or halogen moieties, such as:

Alternately, some moieties that provide aqueous solubility might includehydroxyls, amines, carboxyls, or other hydrophilic or polar moieties.

The above alkoxyamine reagents have a primary amine in the aminooxymoiety. An alkoxyamine reagent can have a secondary amine in theaminooxy moiety. For example, an alkoxyamine reagent can have thestructure

In particular configurations of the methods or compositions set forthherein, an alkoxyamine reagent having the structure R2-ONH₂ can beattached to a solid support. In embodiments, the reagent that comprisesthe structure R2-ONH₂ is attached to a solid support in contact with theaqueous solution. For example, the reagent can be attached via thenitrogen atom by substituting one of the hydrogens with a linkage to thesolid support. A benefit of using solid support attached reagent is thatthe reaction will yield a solid support attached product that can bepurified from reactants and other reaction components by separating thesolid support from the liquid where the reaction occurred. Attachment ofthe reagent to the solid support can also occur via a linkage to the R2moiety.

Generally, a solution that is used to synthesize a nucleotide having a3′-ONH₂ moiety using an alkoxyamine reagent set forth herein can have apH of 4 to 8. As the pH decreases in this range, the rate of convertingthe 3′-O-oxime moiety of a nucleotide to 3′-O—NH₂ moiety increases.However, as pH approaches the lower end of the range the risk of sidereactions that cause unwanted modification to other moieties of thenucleotide also increases. Accordingly, pH for a synthetic reaction setforth herein can be in a range from 5 to 8, 6 to 8, or 7 to 8. Ifdesired the pH can be in a range of 4 to 7, 4 to 6, or 4 to 5, as wellas 5 to 7, 5 to 6, or 6 to 7, or any upper and lower range valueencompassed by the range of lower and upper pH values disclosed herein.Similarly pH for a synthetic reaction set forth herein can be at least4, at least 5, at least 6, at least 7, or no more than 8, no more than7, no more than 6, or no more than 5.

Nucleotides having reversible terminators other than 3′-O-oxime or3′-ONH₂ can be used in a method or composition herein. For example,nucleotides having different types of reversible terminators can beuseful when it is desired to block a population of primers such that oneor more subpopulation of the primers can be selectively deblocked. Morespecifically, a first subpopulation of primers can be blocked with a3′-O-oxime or 3′-ONH₂ moiety and a second population can be blocked witha second type of blocking moiety. The second type of blocking moietycan, advantageously be deblocked by a method that is orthogonal to thedeblocking methods set forth herein for the 3′-O-oxime or 3′-ONH₂moiety. Orthogonal methods are those that do not substantially crossreact. Accordingly, the 3′-O-oxime or 3′-ONH₂ moiety can be deblocked bya method that does not substantially deblock the second blocking moiety,and the second blocking moiety can be deblocked by a method that doesnot substantially deblock the 3′-O-oxime or 3′-ONH₂ moiety,respectively.

Examples of other types of reversible terminator moieties and theirdeblocking methods include, but are not limited to, the following.Useful reversible terminator moieties include those that can bechemically deblocked such as 3′ azidomethyl which can be removed byphosphines, esters which can be deblocked by base hydrolysis or metalcatalysts, and others set forth in U.S. Pat. Nos. 7,427,673; 7,414,116;7,057,026; 7,544,794 or 8,034,923; or PCT publications WO 91/06678 or WO07/123744, each of which is incorporated herein by reference. Otheruseful reversible terminators include 3′ photoreactive moieties that canbe removed by light such as those described in U.S. Pat. Nos. 7,964,352;9,399,798 and 10,041,115 (each of which is incorporated herein byreference in its entirety), or enzymatically removable moieties such as3′ phosphate moieties that can be removed by phosphatases such as thoseset forth in U.S. Pat. No. 10,378,051 (which is incorporated herein byreference in its entirety).

Nucleotides having irreversible terminators can be used in a method orcomposition herein. For example, nucleotides having irreversibleterminators can be useful when it is desired to block a population ofprimers such that a first subpopulation of the primers can be deblockedand a second subpopulation is resistant to deblocking. Morespecifically, a first subpopulation of primers can be blocked with a3′-ONH₂ moiety and a second population can be blocked with anirreversible blocking moiety. Irreversible nucleotides include 2′,3′-dideoxynucleotides (ddNTPs such as ddGTP, ddATP, ddTTP, ddCTP).Dideoxynucleotides lack the 3′-OH group of dNTPs that would otherwiseparticipate in polymerase-mediated or ligase-mediated primer extension.Thus, the 3′ position has a hydrogen moiety instead of the nativehydroxyl moiety.

Nucleotides that are used for particular configurations of the methodsand compositions herein, for example, to participate in stabilizedternary complexes, need not include blocking groups (e.g. reversibleterminators) that prevent subsequent nucleotide incorporation at the3′-end of the primer after the analog has been incorporated into theprimer. This can be the case whether or not an extension step is carriedout using nucleotide(s) having a blocking group such as a reversibleterminator.

A nucleotide that is a constituent of compositions herein or producedthrough method herein, for example, during synthesis procedures orduring a sequencing process, can optionally include an exogenous label.An exogenously labeled nucleotide can include a reversible orirreversible terminator moiety, an exogenously labeled nucleotide can benon-incorporable, an exogenously labeled nucleotide can lack terminatormoieties, an exogenously labeled nucleotide can be incorporable or anexogenously labeled nucleotide can be both incorporable andnon-terminated. An exogenously labeled nucleotide can be a moiety in anucleic acid, for example, being the 3′ nucleotide of a primer.Exogenously labeled nucleotides can be particularly useful in aSequencing By Binding™ process when used to form a stabilized ternarycomplex with a non-labeled polymerase. Exogenously labeled nucleotidescan be useful in a sequencing by synthesis process when incorporatedinto a primer by polymerase.

Examples of useful exogenous labels include, but are not limited to,radiolabel moieties, luminophore moieties, fluorophore moieties, quantumdot moieties, chromophore moieties, enzyme moieties, electromagneticspin labeled moieties, nanoparticle light scattering moieties, and anyof a variety of other signal generating moieties known in the art.Suitable enzyme moieties include, for example, horseradish peroxidase,alkaline phosphatase, beta-galactosidase, or acetylcholinesterase.Exemplary fluorophore labels include, but are not limited to rhodols;resorufins; coumarins; xanthenes; acridines; fluoresceins; rhodamines;erythrins; cyanins; phthalaldehydes; naphthylamines; fluorescamines;benzoxadiazoles; stilbenes; pyrenes; indoles; borapolyazaindacenes;quinazolinones; eosin; erythrosin; Malachite green; CY dyes (GEBiosciences), including Cy3 (and its derivatives), Cy5 (and itsderivatives) and Cy7 (and its derivatives); DYOMICS and DYLIGHT dyes(Dyomics) including DY-547, DY-630, DY-631, DY-632, DY-633, DY-634,DY-635, DY-647, DY-649, DY-652, DY-678, DY-680, DY-682, DY-701, DY-734,DY-752, DY-777 and DY-782; Lucifer Yellow; CASCADE BLUE; TEXAS RED;BODIPY (boron-dipyrromethene) (Molecular Probes) dyes including BODIPY630/650 and BODIPY 650/670; ATTO dyes (Atto-Tec) including ATTO 390,ATTO 425, ATTO 465, ATTO 610 611X, ATTO 610, ATTO 635; ALEXA FLUORSincluding ALEXA FLUOR 633, ALEXA FLUOR 647, ALEXA FLUOR 660, ALEXA FLUOR700, ALEXA FLUOR 750, and ALEXA FLUOR 680 (Molecular Probes); DDAO(7-hydroxy-9H-(1,3-dichloro-9,9-dimethylacridin-2-one or any derivativesthereof) (Molecular Probes); QUASAR dyes (Biosearch); IRDYES dyes(LiCor) including IRDYE 700DX (NHS ester), IRDYE 800RS (NHS ester) andIRDYE 800CW (NHS ester); EVOBLUE dyes (Evotech Biosystems); JODA 4 dyes(Applied Biosystems); HILYTE dyes (AnaSpec); MR121 and MR200 dyes(Roche); Hoechst dyes 33258 and 33242 (Invitrogen); FAIR OAKS RED(Molecular Devices); SUNNYVALE RED (Molecular Devices); LIGHT CYCLER RED(Roche); EPOCH (Glen Research) dyes including EPOCH REDMOND RED, EPOCHYAKIMA YELLOW, EPOCH GIG HARBOR GREEN; Tokyo green (M. Kamiya, et al.,2005 Angew. Chem. Int. Ed. 44:5439-5441); and CF dyes including CF 647and CF555 (Biotium), and others known in the art such as those describedin Principles of Fluorescence Spectroscopy, Joseph R. Lakowicz (Editor),Plenum Pub Corp, 2nd edition (July 1999) and the 6th Edition ofMolecular Probes Handbook by Richard P. Hoagland. In embodiments, anexogenous label is a detectable moiety. In embodiments, an exogenouslabel is a detectable agent.

An exogenous label can be attached to a nucleotide or nucleic acid via alinker. A linker that is present in a nucleotide or nucleic acid can be,but need not be, cleavable. For example, the exogenous label can beattached to the nucleobase of a nucleotide or nucleic acid via a linkerand the linker can be inert to an alkoxyamine reagent having formulaR2-ONH₂ and or the linker can be inert to nitrous acid (HONO). Thelinker can be stable to conditions used in methods set forth herein suchthat the covalent structure of the linker is not changed during anyparticular step, or throughout all steps, of a method set forth herein.Alternatively, the linker that attaches an exogenous label to anucleobase can be reactive with an alkoxyamine reagent having formulaR2-ONH₂ such that the reaction detaches the exogenous label from thenucleobase. For example, the linker can include a moiety having thestructure:

wherein at least one of R3, R4 or R5 is attached to the exogenous labeldirectly or via a second moiety of the linker and wherein at least oneof R3, R4 or R5 is attached to the nucleobase directly or via a thirdmoiety of the linker. Another useful linker moiety is a hydrazone. Forexample, the linker can include a moiety having the structure:

wherein at least one of R3, R4 or R5 is attached to the exogenous labeldirectly or via a second moiety of the linker and wherein at least oneof R3, R4 or R5 is attached to the nucleobase directly or via a thirdmoiety of the linker. These linker moieties can be reacted with anR2-ONH₂ molecule to cleave the exogenous label from the nucleobase. Inembodiments, B, Base, R3, R4, R5, R6, R7, or R8 may independentlyinclude an exogenous label. In embodiments, B, Base, R3, R4, R5, R6, R7,or R8 may independently include a label. In embodiments, B, Base, R3,R4, R5, R6, R7, or R8 may independently include a detectable moiety. Inembodiments, B, Base, R3, R4, R5, R6, R7, or R8 may independentlyinclude a fluorphore moiety. In embodiments, R3, R4, R5, R6, R7, or R8independently is an exogenous label. In embodiments, R3, R4, R5, R6, R7,or R8 independently is a label. In embodiments, R3, R4, R5, R6, R7, orR8 independently is a detectable moiety. In embodiments, R3, R4, R5, R6,R7, or R8 independently is a fluorphore moiety. In embodiments, theblocking moiety is an exogenous label moiety. In embodiments, theblocking moiety includes an exogenous label moiety. In embodiments, theprotecting moiety is an exogenous label moiety. In embodiments, theprotecting moiety includes an exogenous label moiety.

R5 is independently H, CH₃, alkyl, alkenyl, alkynyl, cycloalkyl,cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl,heteroaralkyl, (heteroalicyclyl)alkyl, or an optionally substitutedvariant thereof, or an exogenous label moiety.

In embodiments, a substituted R5 (e.g., substituted alkyl, substitutedalkenyl, substituted alkynyl, substituted cycloalkyl, substitutedcycloalkenyl, substituted cycloalkynyl, substituted aryl, substitutedheteroaryl, substituted heteroalicyclyl, substituted aralkyl,substituted heteroaralkyl, and/or substituted (heteroalicyclyl)alkyl) issubstituted with at least one substituent group, size-limitedsubstituent group, or lower substituent group; wherein if thesubstituted R5 is substituted with a plurality of groups selected fromsubstituent groups, size-limited substituent groups, and lowersubstituent groups; each substituent group, size-limited substituentgroup, and/or lower substituent group may optionally be different. Inembodiments, when R5 is substituted, it is substituted with at least onesubstituent group. In embodiments, when R5 is substituted, it issubstituted with at least one size-limited substituent group. Inembodiments, when R5 is substituted, it is substituted with at least onelower substituent group.

In embodiments, R5 is independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof. In embodiments, R5 isindependently an exogenous label moiety.

In alternative embodiments, a nucleotide, nucleic acid, reactant for amethod set forth herein or product of a method set forth herein can lackexogenous labels. For example, a nucleic acid, nucleotide, polymeraseand/or stabilized ternary complex can lack one, several or all of theexogenous labels described herein or in the references that are citedand incorporated herein. For example, a non-labeled ternary complex canbe detected based on intrinsic properties of the stabilized ternarycomplex, such as mass, charge, intrinsic optical properties or the like.Exemplary methods for detecting non-labeled ternary complexes are setforth in commonly owned U.S. Pat. App. Pub. Nos. 2017/0191125 A1 or2017/0022553 A1; or U.S. Pat. No. 10,246,744, each of which isincorporated herein by reference.

In embodiments, the nucleobase includes an exogenous label moiety (e.g.,connected to the nucleobase through a linker, a fluorophore moiety, anantigen for antibody recognition). In embodiments, the nucleobase issubstituted with an exogenous label moiety (e.g., connected to thenucleobase through a linker, a fluorophore moiety, an antigen forantibody recognition). In embodiments, the nucleobase is covalentlybonded to the exogenous label moiety through a linker. In embodiments,the linker includes

In embodiments, the linker includes

In embodiments, the linker is

In embodiments, the linker is

L3 and L5 are each independently a covalent linker. In embodiments, L5is bonded to a nucleobase. In embodiments, L3 is bonded to a nucleobase.In embodiments L5 is bonded to an exogenous label moiety. Inembodiments, L3 is bonded to an exogenous label moiety. In embodiments,L5 is-L5A-L5B-L5C-L5D-L5E-. In embodiments, L3 is -L3A-L3B-L3C-L3D-L3E-.In embodiment, the linker connecting the nucleobase to the exogenouslabel moiety is -L6-L7-L8-L9-L10-. L3A, L3B, L3C, L3D, L3E, L5A, L5B,L5C, L5D, L5E, L6, L7, L8, L9, and L10 are independently a bond, —NH—,—O—, —S—, —SO₂—, —C(O)—, —C(O)NH—, —NHC(O)—, —NHC(O)NH—, —C(O)O—, —OC(O)—, —SO₂NH—, —NHSO₂—, substituted or unsubstituted alkylene (e.g.,C₁-C₈, C₁-C₆, or C₁-C₄), substituted or unsubstituted alkenylene (e.g.,C₂-C₈, C₂-C₆, or C2-C4), substituted or unsubstituted alkynylene (e.g.,C₂-C₈, C₂-C₆, or C₂-C₄), substituted or unsubstituted heteroalkylene(e.g., 2 to 8 membered, 2 to 6 membered, or 2 to 4 membered),substituted or unsubstituted cycloalkylene (e.g., C₃-C₈, C₃-C₆, orC5-C6), substituted or unsubstituted cycloalkenylene (e.g., C₃-C₈,C₃-C₆, or C₅-C₆), substituted or unsubstituted cycloalkynylene (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆), substituted or unsubstituted arylene (e.g.,C₆-C₁₀ aryl, C₁₀ aryl, or phenylene), substituted or unsubstitutedheteroarylene (e.g., 5 to 10 membered, 5 to 9 membered, or 5 to 6membered), substituted or unsubstituted heteroalicyclylene (e.g., 3 to 8membered, 3 to 6 membered, or 5 to 6 membered), substituted orunsubstituted aralkylene, substituted or unsubstituted heteroaralkylene,or substituted or unsubstituted (heteroalicyclyl)alkylene.

In embodiments, L3 is substituted. In embodiments, L3 is unsubstituted.In embodiments, a substituted L3 (e.g., a substituted covalent linker)is substituted with at least one substituent group, size-limitedsubstituent group, or lower substituent group; wherein if thesubstituted L3 is substituted with a plurality of groups selected fromsubstituent groups, size-limited substituent groups, and lowersubstituent groups; each substituent group, size-limited substituentgroup, and/or lower substituent group may optionally be different. Inembodiments, when L3 is substituted, it is substituted with at least onesubstituent group. In embodiments, when L3 is substituted, it issubstituted with at least one size-limited substituent group. Inembodiments, when L3 is substituted, it is substituted with at least onelower substituent group.

In embodiments, L5 is substituted. In embodiments, L5 is unsubstituted.In embodiments, a substituted L5 (e.g., a substituted covalent linker)is substituted with at least one substituent group, size-limitedsubstituent group, or lower substituent group; wherein if thesubstituted L5 is substituted with a plurality of groups selected fromsubstituent groups, size-limited substituent groups, and lowersubstituent groups; each substituent group, size-limited substituentgroup, and/or lower substituent group may optionally be different. Inembodiments, when L5 is substituted, it is substituted with at least onesubstituent group. In embodiments, when L5 is substituted, it issubstituted with at least one size-limited substituent group. Inembodiments, when L5 is substituted, it is substituted with at least onelower substituent group.

In embodiments, a substituted L3A (e.g., substituted alkylene,substituted alkenylene, substituted alkynylene, substitutedheteroalkylene, substituted cycloalkylene, substituted cycloalkenylene,substituted cycloalkynylene, substituted arylene, substitutedheteroarylene, substituted heteroalicyclylene, substituted aralkylene,substituted heteroaralkylene, and/or substituted(heteroalicyclyl)alkylene) is substituted with at least one substituentgroup, size-limited substituent group, or lower substituent group;wherein if the substituted L3A is substituted with a plurality of groupsselected from substituent groups, size-limited substituent groups, andlower substituent groups; each substituent group, size-limitedsubstituent group, and/or lower substituent group may optionally bedifferent. In embodiments, when L3A is substituted, it is substitutedwith at least one substituent group. In embodiments, when L3A issubstituted, it is substituted with at least one size-limitedsubstituent group. In embodiments, when L3A is substituted, it issubstituted with at least one lower substituent group.

In embodiments, a substituted L3B (e.g., substituted alkylene,substituted alkenylene, substituted alkynylene, substitutedheteroalkylene, substituted cycloalkylene, substituted cycloalkenylene,substituted cycloalkynylene, substituted arylene, substitutedheteroarylene, substituted heteroalicyclylene, substituted aralkylene,substituted heteroaralkylene, and/or substituted(heteroalicyclyl)alkylene) is substituted with at least one substituentgroup, size-limited substituent group, or lower substituent group;wherein if the substituted L3B is substituted with a plurality of groupsselected from substituent groups, size-limited substituent groups, andlower substituent groups; each substituent group, size-limitedsubstituent group, and/or lower substituent group may optionally bedifferent. In embodiments, when L3B is substituted, it is substitutedwith at least one substituent group. In embodiments, when L3B issubstituted, it is substituted with at least one size-limitedsubstituent group. In embodiments, when L3B is substituted, it issubstituted with at least one lower substituent group.

In embodiments, a substituted L3C (e.g., substituted alkylene,substituted alkenylene, substituted alkynylene, substitutedheteroalkylene, substituted cycloalkylene, substituted cycloalkenylene,substituted cycloalkynylene, substituted arylene, substitutedheteroarylene, substituted heteroalicyclylene, substituted aralkylene,substituted heteroaralkylene, and/or substituted(heteroalicyclyl)alkylene) is substituted with at least one substituentgroup, size-limited substituent group, or lower substituent group;wherein if the substituted L3C is substituted with a plurality of groupsselected from substituent groups, size-limited substituent groups, andlower substituent groups; each substituent group, size-limitedsubstituent group, and/or lower substituent group may optionally bedifferent. In embodiments, when L3C is substituted, it is substitutedwith at least one substituent group. In embodiments, when L3C issubstituted, it is substituted with at least one size-limitedsubstituent group. In embodiments, when L3C is substituted, it issubstituted with at least one lower substituent group.

In embodiments, a substituted L3D (e.g., substituted alkylene,substituted alkenylene, substituted alkynylene, substitutedheteroalkylene, substituted cycloalkylene, substituted cycloalkenylene,substituted cycloalkynylene, substituted arylene, substitutedheteroarylene, substituted heteroalicyclylene, substituted aralkylene,substituted heteroaralkylene, and/or substituted(heteroalicyclyl)alkylene) is substituted with at least one substituentgroup, size-limited substituent group, or lower substituent group;wherein if the substituted L3D is substituted with a plurality of groupsselected from substituent groups, size-limited substituent groups, andlower substituent groups; each substituent group, size-limitedsubstituent group, and/or lower substituent group may optionally bedifferent. In embodiments, when L3D is substituted, it is substitutedwith at least one substituent group. In embodiments, when L3D issubstituted, it is substituted with at least one size-limitedsubstituent group. In embodiments, when L3D is substituted, it issubstituted with at least one lower substituent group.

In embodiments, a substituted L3E (e.g., substituted alkylene,substituted alkenylene, substituted alkynylene, substitutedheteroalkylene, substituted cycloalkylene, substituted cycloalkenylene,substituted cycloalkynylene, substituted arylene, substitutedheteroarylene, substituted heteroalicyclylene, substituted aralkylene,substituted heteroaralkylene, and/or substituted(heteroalicyclyl)alkylene) is substituted with at least one substituentgroup, size-limited substituent group, or lower substituent group;wherein if the substituted L3E is substituted with a plurality of groupsselected from substituent groups, size-limited substituent groups, andlower substituent groups; each substituent group, size-limitedsubstituent group, and/or lower substituent group may optionally bedifferent. In embodiments, when L3E is substituted, it is substitutedwith at least one substituent group. In embodiments, when L3E issubstituted, it is substituted with at least one size-limitedsubstituent group. In embodiments, when L3E is substituted, it issubstituted with at least one lower substituent group.

In embodiments, a substituted L5A (e.g., substituted alkylene,substituted alkenylene, substituted alkynylene, substitutedheteroalkylene, substituted cycloalkylene, substituted cycloalkenylene,substituted cycloalkynylene, substituted arylene, substitutedheteroarylene, substituted heteroalicyclylene, substituted aralkylene,substituted heteroaralkylene, and/or substituted(heteroalicyclyl)alkylene) is substituted with at least one substituentgroup, size-limited substituent group, or lower substituent group;wherein if the substituted L5A is substituted with a plurality of groupsselected from substituent groups, size-limited substituent groups, andlower substituent groups; each substituent group, size-limitedsubstituent group, and/or lower substituent group may optionally bedifferent. In embodiments, when L5A is substituted, it is substitutedwith at least one substituent group. In embodiments, when L5A issubstituted, it is substituted with at least one size-limitedsubstituent group. In embodiments, when L5A is substituted, it issubstituted with at least one lower substituent group.

In embodiments, a substituted L5B (e.g., substituted alkylene,substituted alkenylene, substituted alkynylene, substitutedheteroalkylene, substituted cycloalkylene, substituted cycloalkenylene,substituted cycloalkynylene, substituted arylene, substitutedheteroarylene, substituted heteroalicyclylene, substituted aralkylene,substituted heteroaralkylene, and/or substituted(heteroalicyclyl)alkylene) is substituted with at least one substituentgroup, size-limited substituent group, or lower substituent group;wherein if the substituted L5B is substituted with a plurality of groupsselected from substituent groups, size-limited substituent groups, andlower substituent groups; each substituent group, size-limitedsubstituent group, and/or lower substituent group may optionally bedifferent. In embodiments, when L5B is substituted, it is substitutedwith at least one substituent group. In embodiments, when L5B issubstituted, it is substituted with at least one size-limitedsubstituent group. In embodiments, when L5B is substituted, it issubstituted with at least one lower substituent group.

In embodiments, a substituted L5C (e.g., substituted alkylene,substituted alkenylene, substituted alkynylene, substitutedheteroalkylene, substituted cycloalkylene, substituted cycloalkenylene,substituted cycloalkynylene, substituted arylene, substitutedheteroarylene, substituted heteroalicyclylene, substituted aralkylene,substituted heteroaralkylene, and/or substituted(heteroalicyclyl)alkylene) is substituted with at least one substituentgroup, size-limited substituent group, or lower substituent group;wherein if the substituted L5C is substituted with a plurality of groupsselected from substituent groups, size-limited substituent groups, andlower substituent groups; each substituent group, size-limitedsubstituent group, and/or lower substituent group may optionally bedifferent. In embodiments, when L5C is substituted, it is substitutedwith at least one substituent group. In embodiments, when L5C issubstituted, it is substituted with at least one size-limitedsubstituent group. In embodiments, when L5C is substituted, it issubstituted with at least one lower substituent group.

In embodiments, a substituted L5D (e.g., substituted alkylene,substituted alkenylene, substituted alkynylene, substitutedheteroalkylene, substituted cycloalkylene, substituted cycloalkenylene,substituted cycloalkynylene, substituted arylene, substitutedheteroarylene, substituted heteroalicyclylene, substituted aralkylene,substituted heteroaralkylene, and/or substituted(heteroalicyclyl)alkylene) is substituted with at least one substituentgroup, size-limited substituent group, or lower substituent group;wherein if the substituted L5D is substituted with a plurality of groupsselected from substituent groups, size-limited substituent groups, andlower substituent groups; each substituent group, size-limitedsubstituent group, and/or lower substituent group may optionally bedifferent. In embodiments, when L5D is substituted, it is substitutedwith at least one substituent group. In embodiments, when L5D issubstituted, it is substituted with at least one size-limitedsubstituent group. In embodiments, when L5D is substituted, it issubstituted with at least one lower substituent group.

In embodiments, a substituted L5E (e.g., substituted alkylene,substituted alkenylene, substituted alkynylene, substitutedheteroalkylene, substituted cycloalkylene, substituted cycloalkenylene,substituted cycloalkynylene, substituted arylene, substitutedheteroarylene, substituted heteroalicyclylene, substituted aralkylene,substituted heteroaralkylene, and/or substituted(heteroalicyclyl)alkylene) is substituted with at least one substituentgroup, size-limited substituent group, or lower substituent group;wherein if the substituted L5E is substituted with a plurality of groupsselected from substituent groups, size-limited substituent groups, andlower substituent groups; each substituent group, size-limitedsubstituent group, and/or lower substituent group may optionally bedifferent. In embodiments, when L5E is substituted, it is substitutedwith at least one substituent group. In embodiments, when L5E issubstituted, it is substituted with at least one size-limitedsubstituent group. In embodiments, when L5E is substituted, it issubstituted with at least one lower substituent group.

In embodiments, a substituted L6 (e.g., substituted alkylene,substituted alkenylene, substituted alkynylene, substitutedheteroalkylene, substituted cycloalkylene, substituted cycloalkenylene,substituted cycloalkynylene, substituted arylene, substitutedheteroarylene, substituted heteroalicyclylene, substituted aralkylene,substituted heteroaralkylene, and/or substituted(heteroalicyclyl)alkylene) is substituted with at least one substituentgroup, size-limited substituent group, or lower substituent group;wherein if the substituted L6 is substituted with a plurality of groupsselected from substituent groups, size-limited substituent groups, andlower substituent groups; each substituent group, size-limitedsubstituent group, and/or lower substituent group may optionally bedifferent. In embodiments, when L6 is substituted, it is substitutedwith at least one substituent group. In embodiments, when L6 issubstituted, it is substituted with at least one size-limitedsubstituent group. In embodiments, when L6 is substituted, it issubstituted with at least one lower substituent group.

In embodiments, a substituted L7 (e.g., substituted alkylene,substituted alkenylene, substituted alkynylene, substitutedheteroalkylene, substituted cycloalkylene, substituted cycloalkenylene,substituted cycloalkynylene, substituted arylene, substitutedheteroarylene, substituted heteroalicyclylene, substituted aralkylene,substituted heteroaralkylene, and/or substituted(heteroalicyclyl)alkylene) is substituted with at least one substituentgroup, size-limited substituent group, or lower substituent group;wherein if the substituted L7 is substituted with a plurality of groupsselected from substituent groups, size-limited substituent groups, andlower substituent groups; each substituent group, size-limitedsubstituent group, and/or lower substituent group may optionally bedifferent. In embodiments, when L7 is substituted, it is substitutedwith at least one substituent group. In embodiments, when L7 issubstituted, it is substituted with at least one size-limitedsubstituent group. In embodiments, when L7 is substituted, it issubstituted with at least one lower substituent group.

In embodiments, a substituted L8 (e.g., substituted alkylene,substituted alkenylene, substituted alkynylene, substitutedheteroalkylene, substituted cycloalkylene, substituted cycloalkenylene,substituted cycloalkynylene, substituted arylene, substitutedheteroarylene, substituted heteroalicyclylene, substituted aralkylene,substituted heteroaralkylene, and/or substituted(heteroalicyclyl)alkylene) is substituted with at least one substituentgroup, size-limited substituent group, or lower substituent group;wherein if the substituted L8 is substituted with a plurality of groupsselected from substituent groups, size-limited substituent groups, andlower substituent groups; each substituent group, size-limitedsubstituent group, and/or lower substituent group may optionally bedifferent. In embodiments, when L8 is substituted, it is substitutedwith at least one substituent group. In embodiments, when L8 issubstituted, it is substituted with at least one size-limitedsubstituent group. In embodiments, when L8 is substituted, it issubstituted with at least one lower substituent group.

In embodiments, a substituted L9 (e.g., substituted alkylene,substituted alkenylene, substituted alkynylene, substitutedheteroalkylene, substituted cycloalkylene, substituted cycloalkenylene,substituted cycloalkynylene, substituted arylene, substitutedheteroarylene, substituted heteroalicyclylene, substituted aralkylene,substituted heteroaralkylene, and/or substituted(heteroalicyclyl)alkylene) is substituted with at least one substituentgroup, size-limited substituent group, or lower substituent group;wherein if the substituted L9 is substituted with a plurality of groupsselected from substituent groups, size-limited substituent groups, andlower substituent groups; each substituent group, size-limitedsubstituent group, and/or lower substituent group may optionally bedifferent. In embodiments, when L9 is substituted, it is substitutedwith at least one substituent group. In embodiments, when L9 issubstituted, it is substituted with at least one size-limitedsubstituent group. In embodiments, when L9 is substituted, it issubstituted with at least one lower substituent group.

In embodiments, a substituted L10 (e.g., substituted alkylene,substituted alkenylene, substituted alkynylene, substitutedheteroalkylene, substituted cycloalkylene, substituted cycloalkenylene,substituted cycloalkynylene, substituted arylene, substitutedheteroarylene, substituted heteroalicyclylene, substituted aralkylene,substituted heteroaralkylene, and/or substituted(heteroalicyclyl)alkylene) is substituted with at least one substituentgroup, size-limited substituent group, or lower substituent group;wherein if the substituted L10 is substituted with a plurality of groupsselected from substituent groups, size-limited substituent groups, andlower substituent groups; each substituent group, size-limitedsubstituent group, and/or lower substituent group may optionally bedifferent. In embodiments, when L10 is substituted, it is substitutedwith at least one substituent group. In embodiments, when L10 issubstituted, it is substituted with at least one size-limitedsubstituent group. In embodiments, when L10 is substituted, it issubstituted with at least one lower substituent group.

Alternatively, a nucleotide that is used herein, for example, forextension of a primer or to participate in forming a ternary complex canlack exogenous labels (i.e. the nucleotide can be “non-labeled”). Anon-labeled nucleotide can include a reversible terminator such as a3′-ONH₂ moiety or an irreversible terminator moiety. A non-labelednucleotide can be non-incorporable, a non-labeled nucleotide can lackterminator moieties, a non-labeled nucleotide can be incorporable, or anon-labeled nucleotide can be both incorporable and non-terminated.Non-labeled nucleotides can be useful, for example, in a Sequencing ByBinding™ (SBB^(M)) process when a label on a polymerase is used todetect a stabilized ternary complex or when label-free detection isused. Non-labeled nucleotides can also be useful in an extension step ofa SBB™ method or other method set forth herein. It will be understoodthat absence of a moiety or function for a nucleotide refers to thenucleotide having no such function or moiety. However, it will also beunderstood that one or more of the functions or moieties set forthherein for a nucleotide, or analog thereof, or otherwise known in theart for a nucleotide, or analog thereof, can be specifically omitted ina method or composition set forth herein.

The nucleobase of a nucleotide can be a purine or pyrimidine. Forexample, the nucleobase can be a canonical or primary nucleobase such asadenine, cytosine, guanine, thymine, or uracil. Other nucleobases can beuseful such as those that are complementary to one or more of theprimary or canonical nucleobases. In embodiments, the nucleobase iscomplementary to adenine, cytosine, guanine, thymine, or uracil.Modified nucleotides can be used, for example, methylated nucleobasessuch as 5-methylcytosine or 7-methylguanosine, or hydroxylated andmethylated nucleobases such as 5-hydroxymethylcytosine. Other usefulnucleobases include, for example, hypoxanthine, xanthine, inosine,isoguanine or isocytosine. Isoguanine and isocytosine can beparticularly useful since they are complementary to each other, andspecific for each other so as to form a third base pair when compared tothe two native base pairs, Adenine:Thymine and Cytosine:Guanine. Aparticularly useful nucleobase is 7-deazaguanine, which can provide aconvenient nucleobase for synthetic procedures that attach a label tothe nucleobase while also being capable of pairing with cytosine whenthe labeled nucleobase is present in a nucleic acid strand. Inembodiments, the nucleobase is independently 5-methylcytosine,hypoxanthine, xanthine, inosine, isoguanine, isocytosine, or7-deazaguanine. In embodiments, the nucleobase (e.g., B, Base) includesan exogenous label (e.g., detectable moiety, fluorophore moiety,antigen) optionally bonded directly to the nucleobase or optionallybonded through a linker (e.g., L5).

The sugar moiety of a nucleotide can be a deoxyribose, ribose or analogthereof. For example, a nucleotide can have one of the followingstructures:

wherein R1 is H, B is a nucleobase and R3 and R4 are independently H,CH₃, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl,aryl, heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl,(heteroalicyclyl)alkyl, or an optionally substituted variant thereof.This deoxyribonucleotide can be in a monomeric form whereby Q is ahydrogen, exogenous protecting moiety, or at least one phosphate (e.g.monophosphate, diphosphate, triphosphate or greater than threephosphates, any of the preceding which can be substituted orunsubstituted). Alternatively, the nucleotide can be a moiety of anucleic acid, for example, wherein Q is a deoxyribonucleic acid (DNA).The DNA can be single stranded or double stranded. In configurations inwhich the DNA is double stranded the nucleotide can be a moiety of aprimer strand, for example, being at the 3′ end of the primer, or thenucleotide moiety can be in the template strand. The nucleotide can be amoiety of a nucleic acid that is a mixed hybrid formed by strands havingdifferent backbones such as a DNA:RNA hybrid, DNA:PNA hybrid, RNA:PNAhybrid or the like (wherein PNA is peptide nucleic acid).

Alternatively, the sugar moiety of a nucleotide can have one of thefollowing structures:

wherein R1 is OH, B is a nucleobase and R3 and R4 are independently H,CH₃, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl,aryl, heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl,(heteroalicyclyl)alkyl, or an optionally substituted variant thereof.This ribonucleotide can be in a monomeric form whereby Q is at least onephosphate (e.g. monophosphate, diphosphate, triphosphate or greater thanthree phosphates, any of the preceding which can be substituted orunsubstituted). Alternatively, the nucleotide can be a moiety of anucleic acid, for example, wherein Q is a ribonucleic acid (RNA). TheRNA can be single stranded or double stranded. In configurations inwhich the RNA is double stranded the nucleotide can be a moiety of aprimer strand, for example, being at the 3′ end of the primer, or thenucleotide moiety can be in the template strand. The nucleotide can be amoiety of a nucleic acid that is a mixed hybrid formed by strands havingdifferent backbones such as a DNA:RNA hybrid, DNA:PNA hybrid, RNA:PNAhybrid or the like (wherein PNA is peptide nucleic acid).

Nucleic acids that are used in a method or composition herein can be DNAsuch as genomic DNA, synthetic DNA, amplified DNA, complementary DNA(cDNA) or the like. RNA can also be used such as mRNA, ribosomal RNA,tRNA or the like. Nucleic acid analogs such as PNA or others known inthe art can also be used herein. Nucleic acid primers, probes ortemplates can be DNA, RNA or analogs thereof.

A nucleic acid may be single stranded or double stranded. A doublestranded nucleic acid may possess a single-stranded nick or a gap. Wheredouble-stranded, a nucleic acid molecule can be blunt-ended or have anoverhang (e.g. 5′ overhang or 3′ overhang). Such nucleic acid moleculescan be produced by any chemical or enzymatic method known in the art.Examples of such methods include phosphoramidite synthesis orreplication in vivo or in vitro. A nucleic acid of the presentdisclosure can be linear (e.g. having free 3′ and 5′ ends) or it can becircular (e.g. lacking 5′ and 3′ ends)

Deoxyribonucleic acid (DNA) is a particularly useful nucleic acid. TheDNA can be single- or double-stranded deoxyribonucleic acid.Deoxyribonucleotides are typically joined by phosphodiester bonds,although in some cases, nucleic acid analogs are included that may havealternate backbones, such as, phosphoramide (e.g. Beaucage, et al.,Tetrahedron, 49 (10):1925 (1993) and references therein; Letsinger, J.Org. Chem., 35:3800 (1970); Sprinzl, et al., Eur. J. Biochem., 81:579(1977); Letsinger, et al., Nucl. Acids Res., 14:3487 (1986); Sawai, etal., Chem. Lett., 805 (1984), Letsinger, et al., J. Am. Chem. Soc.,110:4470 (1988); and Pauwels, et al., Chemica Scripta, 26:141 (1986)),phosphorothioate (e.g. Mag, et al., Nucleic Acids Res., 19:1437 (1991);and U.S. Pat. No. 5,644,048), phosphorodithioate (e.g. Briu, et al., J.Am. Chem. Soc., 111:2321 (1989)), O-methylphophoroamidite linkages (e.g.Eckstein, Oligonucleotides and Analogues: A Practical Approach, OxfordUniversity Press), and peptide nucleic acid (PNA) backbones and linkages(e.g. Egholm, J. Am. Chem. Soc., 114:1895 (1992); Meier, et al., Chem.Int. Ed. Engl., 31:1008 (1992); Nielsen, Nature, 365:566 (1993);Carlsson, et al., Nature, 380:207 (1996)). Other analog nucleic acidsinclude those with positive backbones (e.g. Denpcy, et al., Proc, Natd.Acad. Sci. USA, 92:6097 (1995)); non-ionic backbones (e.g. U.S. Pat.Nos. 5,386,023; 5,637,684; 5,602,240; 5,216,141; and U.S. Pat. No.4,469,863; Kiedrowshi, et al., Angew. Chem. Intl. Ed. English, 30:423(1991); Letsinger, et al., J Am. Chem. Soc., 110:4470 (1988); Letsinger,et al., Nucleosides & Nucleotides, 13:1597 (1994); Chapters 2 and 3, ASCSymposium Series 580, “Carbohydrate Modifications in AntisenseResearch”, Ed. Y. S. Sanghui and P. Dan Cook; Mesmaeker, et al.,Bioorganic & Medicinal Chem. Lett., 4:395 (1994); Jeffs, et al., J.Biomolecular NMR, 34:17 (1994); Tetrahedron Lett., 37:743 (1996)) andnon-ribose backbones, including for example, those described in U.S.Pat. Nos. 5,235,033 and 5,034,506, and Chapters 6 and 7, ACS SymposiumSeries 580, “Carbohydrate Modifications in Antisense Research”, Ed. Y.S. Sanghui and P. Dan Cook. Nucleic acids containing one or morecarbocyclic sugars are also included within the definition of nucleicacids (e.g. Jenkins, et al., Chem. Soc. Rev., (1995) pp. 169 176).Several nucleic acid analogs are described in Rawls, C & E News, Jun. 2,1997, page 35. All of these references are hereby expressly incorporatedby reference. These modifications of the ribose-phosphate backbone maybe present to facilitate the addition of exogenous moieties such aslabels, or to increase the stability and half-life of such molecules inphysiological environments. In addition, mixtures of naturally occurringnucleic acids and analogs can be made. Alternatively, mixtures ofdifferent nucleic acid analogs, and mixtures of naturally occurringnucleic acid analogs and non-natural analogs may be made.

Exemplary organisms from which nucleic acids can be derived include, forexample, those from a mammal such as a rodent, mouse, rat, rabbit,guinea pig, ungulate, horse, sheep, pig, goat, cow, cat, dog, primate,human or non-human primate; a plant such as Arabidopsis thaliana, corn,sorghum, oat, wheat, rice, canola, or soybean; an algae such asChlamydomonas reinhardtii; a nematode such as Caenorhabditis elegans; aninsect such as Drosophila melanogaster, mosquito, fruit fly, honey beeor spider; a fish such as zebrafish; a reptile; an amphibian such as afrog or Xenopus laevis; a Dictyostelium discoideum; a fungi such asPneumocystis carinii, Takifugu rubripes, yeast, Saccharamoycescerevisiae or Schizosaccharomyces pombe; an aplicomplexan alveolatepathogen such as Plasmodium falciparum; an environmental sample; or anyother eukaryotic, eubacterial or archaeal source. Nucleic acids can alsobe derived from a eubacterial prokaryote such as a bacterium,Escherichia coli, Staphylococci or Mycoplasma pneumoniae; an archaeanprokaryote; a virus such as Hepatitis C virus, a coronavirus, or humanimmunodeficiency virus; or a viroid. Nucleic acids can be derived from ahomogeneous culture or population of the above organisms oralternatively from a collection of several different organisms, forexample, in a community or ecosystem. Nucleic acids can be isolatedusing methods known in the art including, for example, those describedin Sambrook et al., Molecular Cloning: A Laboratory Manual, 3rd edition,Cold Spring Harbor Laboratory, New York (2001) or in Ausubel et al.,Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore,Md. (1998), each of which is incorporated herein by reference. Cells,tissues, biological fluids, proteins and other samples can be obtainedfrom these organisms and used in a composition, apparatus or method setforth herein.

A nucleic acid can be obtained from a preparative method such as genomeisolation, genome fragmentation, gene cloning and/or amplification. Thenucleic acid can be obtained from an amplification technique such aspolymerase chain reaction (PCR), rolling circle amplification (RCA),multiple displacement amplification (MDA) or the like. Amplification canalso be carried out using a method set forth in Sambrook et al.,Molecular Cloning: A Laboratory Manual, 3rd edition, Cold Spring HarborLaboratory, New York (2001) or in Ausubel et al., Current Protocols inMolecular Biology, John Wiley and Sons, Baltimore, Md. (1998), each ofwhich is incorporated herein by reference.

In some configurations of the methods and compositions set forth herein,a single nucleotide or single nucleic acid molecule can be manipulated,modified or detected. The single nucleotide or single nucleic acidmolecule can be in solution phase, or solid phase (e.g. attached to asurface). In some configurations, the single molecule is subjected todetection under conditions wherein individual molecules are resolved onefrom the other (e.g. single molecule sequencing). Alternatively,multiple nucleotides of a particular type or multiple copies of anucleic acid can be made or used. The resulting ensemble can bemanipulated, modified or detected, for example, in a nucleic acidsequencing protocol. For example, a nucleic acid can be amplified insolution or on a surface (e.g. on the inner wall of a flow cell) usingtechniques set forth in further detail below.

In multiplex embodiments, multiple different nucleic acid molecules(i.e. a population having a variety of different sequences) aremanipulated or detected. The molecules can optionally be attached to asurface in a flow cell or other vessel. The nucleic acids can beattached at unique sites on the surface and single nucleic acidmolecules that are spatially distinguishable one from the other can bemanipulated, modified or detected in parallel. Alternatively, thenucleic acids can be amplified on the surface to produce a plurality ofsurface attached ensembles. The ensembles can be spatiallydistinguishable from each other and manipulated, modified or detected inparallel.

A method set forth herein can use any of a variety of nucleic acidamplification techniques. Exemplary techniques that can be used include,but are not limited to, polymerase chain reaction (PCR), rolling circleamplification (RCA), multiple displacement amplification (MDA), bridgeamplification, or random prime amplification (RPA). In particularconfigurations, one or more primers used for amplification can beattached to a surface in a flow cell. In such embodiments, extension ofthe surface-attached primers along template nucleic acids will result incomplementary copies of the templates being attached to the surface.Such amplification methods can be used for analytical purposes such asreal time PCR or quantitative PCR. Alternatively, amplification can beused to prepare nucleic acids for downstream applications such asnucleic acid sequencing. Preparative amplification methods that resultin one or more sites on a solid support, where each site is attached tomultiple copies of a particular nucleic acid template, can be referredto as “clustering” methods. Primers that are used for DNA amplificationtechniques can include a 3′-O-oxime moiety to be converted to areversible terminator moiety as disclosed herein, or a 3′-ONH₂ or otherreversible terminator moiety as disclosed herein such that deprotectionmethods set forth herein can be used to generate a reversibly terminatedprimer suitable for deblocking so as to initiate extension or to controlextension at one or more points in an amplification reaction.

In PCR techniques, one or both primers used for amplification can beattached to a surface. Formats that utilize two species of attachedprimer are often referred to as bridge amplification because doublestranded amplicons form a bridge-like structure between the two attachedprimers that flank the template sequence that has been copied. Exemplaryreagents and conditions that can be used for bridge amplification aredescribed, for example, in U.S. Pat. Nos. 5,641,658 or 7,115,400; U.S.Patent Pub. Nos. 2002/0055100 A1, 2004/0096853 A1, 2004/0002090 A1,2007/0128624 A1 or 2008/0009420 A1, each of which is incorporated hereinby reference. PCR amplification can also be carried out with one of theamplification primers attached to the surface and the second primer insolution. An exemplary format that uses a combination of one solidphase-attached primer and a solution phase primer is known as primerwalking and can be carried out as described in U.S. Pat. No. 9,476,080,which is incorporated herein by reference. Another example is emulsionPCR which can be carried out as described, for example, in Dressman etal., Proc. Natl. Acad. Sci. USA 100:8817-8822 (2003), WO 05/010145, orU.S. Patent Pub. Nos. 2005/0130173 A1 or 2005/0064460 A1, each of whichis incorporated herein by reference. One or both of the primers used ina PCR technique can include a 3′-O-oxime moiety or 3′-ONH₂ moiety, forexample, prior to initiation of amplification or at a point whereamplification is to be stopped or paused. Amplification can proceed bydeblocking the 3′ position using a method set forth herein.

RCA techniques can be used in a method set forth herein. Exemplaryreagents that can be used in an RCA reaction and methods by which RCAcan produce amplicons are described, for example, in Lizardi et al.,Nat. Genet. 19:225-232 (1998) or US Pat. App. Pub. No. 2007/0099208 A1,each of which is incorporated herein by reference. Primers used for RCAcan be in solution or attached to a surface in a flow cell. The primerscan optionally include a 3′-O-oxime moiety or 3′-ONH₂ moiety, forexample, prior to initiation of amplification or at a point whereamplification is to be stopped or paused. Amplification can proceed bydeblocking the 3′ position using a method set forth herein.

MDA techniques can also be used in a method of the present disclosure.Some reagents and useful conditions for MDA are described, for example,in Dean et al., Proc Natl. Acad. Sci. USA 99:5261-66 (2002); Lage etal., Genome Research 13:294-307 (2003); Walker et al., Molecular Methodsfor Virus Detection, Academic Press, Inc., 1995; Walker et al., Nucl.Acids Res. 20:1691-96 (1992); or U.S. Pat. Nos. 5,455,166; 5,130,238; or6,214,587, each of which is incorporated herein by reference. Primersused for MDA can be in solution or attached to a surface in a flow cell.The primers can optionally include a 3′-O-oxime moiety or 3′-ONH₂moiety, for example, prior to initiation of amplification or at a pointwhere amplification is to be stopped or paused. Amplification canproceed by deblocking the 3′ position using a method set forth herein.

Nucleic acid templates that are used in a method or composition hereincan be DNA such as genomic DNA, synthetic DNA, amplified DNA,complementary DNA (cDNA) or the like. RNA can also be used such as mRNA,ribosomal RNA, tRNA or the like. Nucleic acid analogs can also be usedas templates herein. Primers used herein can be DNA, RNA or analogsthereof.

A nucleic acid that is used in a method or composition herein can belinear, for example, being flanked by a 3′ end and a 5′ end.Alternatively, a nucleic acid can be circular, thereby lacking a 3′ and5′ end. Whether linear, circular or in any other conformation, a nucleicacid that is used herein can have a size that is desired for aparticular use or that is a result of manipulations carried out on thenucleic acid. For example, a nucleic acid can have a length that is atleast 50 bases, 100 bases, 1×10³ bases, 1×10⁴ bases, 1×10⁵ bases, 1×10⁶bases or longer. Alternatively or additionally, the nucleic acid lengthcan be at most 1×10⁶ bases, 1×10⁵ bases, 1×10⁴ bases, 1×10³ bases, 100bases, 50 bases or shorter. When a population of nucleic acids is used,the average length for the population can have a lower and/or upperlimit selected from those ranges.

A nucleotide can be attached to a solid support. The nucleotide can bein monomeric form or it can be a moiety of a nucleic acid. Typically,the nucleotide will be attached to the solid support via a moiety otherthan the 3′ position. As such the 3′ position can be blocked ordeblocked as set forth herein. Accordingly, the nucleotide althoughbeing attached to a solid support can be in contact with a solution. Thesolution can contain reagents for blocking or deblocking the solid-phasenucleotide. By way of example, the attached nucleotide can have one ofthe following structures:

wherein Base is a nucleobase, and wherein DNA is independently a singlestranded deoxyribonucleic acid or double stranded deoxyribonucleic acid.Optionally, the nucleotide can be attached to the solid support via theDNA. Alternatively, the sugar can be a ribose instead of deoxyribose,and the nucleotide can be at the 3′ end of RNA instead of DNA. In thiscase the RNA can be single stranded or double stranded. Optionally, thenucleotide can be attached to the solid support via the RNA.

In embodiments, a substituted Base (e.g., a substituted nucleobase) issubstituted with at least one substituent group, size-limitedsubstituent group, or lower substituent group; wherein if thesubstituted Base is substituted with a plurality of groups selected fromsubstituent groups, size-limited substituent groups, and lowersubstituent groups; each substituent group, size-limited substituentgroup, and/or lower substituent group may optionally be different. Inembodiments, when Base is substituted, it is substituted with at leastone substituent group. In embodiments, when Base is substituted, it issubstituted with at least one size-limited substituent group. Inembodiments, when Base is substituted, it is substituted with at leastone lower substituent group.

A particularly useful solid support is an array. Arrays provide anadvantage of multiplex processing of analytes, whereby the multipledifferent types of analytes are manipulated or detected in parallel.Although it is also possible to serially process different types ofanalytes using methods or compositions set forth herein, parallelprocessing can provide cost savings, time savings and uniformity ofassay conditions. An array can include at least 2, 10, 100, 1×10³,1×10⁴, 1×10⁵, 1×10⁶, 1×10⁹, or more different analyte sites.Alternatively or additionally, an array can include at most 1×10⁹,1×10⁶, 1×10⁵, 1×10⁴, 1×10³, 100, 10, 2 or fewer, different analytesites.

An array can be attached to an inner surface of a vessel (e.g. the innerwall of a flow cell) or to a solid support inside of a vessel (e.g. abead or other solid support inside of a flow cell). The vessel or solidsupport can be made from any of a variety of materials used foranalytical biochemistry. Suitable materials may include glass, polymericmaterials, silicon, quartz (fused silica), borofloat glass, silica,silica-based materials, carbon, metals, an optical fiber or bundle ofoptical fibers, sapphire, or plastic materials. The material can beselected based on properties desired for a particular use. For example,materials that are transparent to a desired wavelength of radiation areuseful for analytical techniques that will utilize radiation at thatwavelength. Conversely, it may be desirable to select a material thatdoes not pass radiation of a certain wavelength (e.g. being opaque,absorptive or reflective). Other properties of a material that can beexploited are inertness or reactivity to reagents used in a downstreamprocess, such as those set forth herein, or ease of manipulation, or lowcost of manufacture.

A particularly useful solid support for use in a flow cell or othervessel is a particle such as a bead or microsphere. Populations of beadscan be used for attachment of populations of analytes such asnucleotides, nucleic acids, reversibly terminated primers, deblockedprimers, extendable primers, polymerases, stabilized ternary complexesor the like. In some configurations, each bead has a single type ofstabilized ternary complex, a single type of component capable offorming the complex, or a single type of some other analyte set forthherein or in references cited herein. For example, an individual beadcan be attached to a single type of ternary complex, a single type oftemplate allele, a single type of template locus, a single type ofprimer, single type of reversibly terminated primer, single type ofdeblocked primer, single type of extendable primer, or a single type ofnucleotide. Alternatively, different types of components need not beseparated on a bead-by-bead basis. As such, a single bead can bearmultiple different types of: ternary complexes, template nucleic acids,primers (whether blocked or extendable), primed template nucleic acids(whether the primers are blocked or extendable) and/or nucleotides(whether blocked or extendable). The composition of a bead can vary,depending for example, on the format, chemistry and/or method ofattachment to be used. Exemplary bead compositions include solidsupports, and chemical functionalities thereon, used in protein andnucleic acid capture methods. Such compositions include, for example,plastics, ceramics, glass, polystyrene, melamine, methylstyrene, acrylicpolymers, paramagnetic materials, thoria sol, carbon graphite, titaniumdioxide, controlled pore glass (CPG), latex or cross-linked dextranssuch as Sepharose™, cellulose, nylon, cross-linked micelles and Teflon™,as well as other materials set forth in “Microsphere Detection Guide”from Bangs Laboratories, Fishers Ind., which is incorporated herein byreference.

Beads can have a symmetrical shape, such as spherical, polyhedral,cylindrical or the like. Alternatively, beads can have an irregular ornon-symmetric shape. Exemplary sizes for beads used herein can haveaverage diameter that is at least about 10 nm, 100 nm, 1 μm, 5 μm, 10μm, 100 μm, 1 mm or larger. Alternatively or additionally, beads usedherein can have average diameter that is at most about 1 mm, 100 μm, 10μm, 5 μm, 1 μm, 100 nm, 10 nm, 1 nm or smaller. Beads in these sizeranges can be used as array features or as particles in a fluid.

Exemplary compositions and techniques that can be used to make an arrayof beads include, without limitation, those used for BeadChip™ Arraysavailable from Illumina, Inc. (San Diego, Calif.) those described inU.S. Pat. Nos. 6,266,459; 6,355,431; 6,770,441; 6,859,570; or 7,622,294;or PCT Publication No. WO 00/63437, each of which is incorporated hereinby reference. Beads can be located at discrete locations, such as wells,on a solid support, whereby each location accommodates a single bead.Alternatively, discrete locations where beads reside can each include aplurality of beads as described, for example, in U.S. Pat. App. Pub.Nos. 2004/0263923 A1, 2004/0233485 A1, 2004/0132205 A1, or 2004/0125424A1, each of which is incorporated herein by reference.

Other useful arrays include those that are used in nucleic acidsequencing applications. For example, arrays that are used to immobilizeamplicons of genomic fragments (often referred to as clusters) can beparticularly useful. Examples of nucleic acid sequencing arrays that canbe used herein include those described in Bentley et al., Nature456:53-59 (2008), PCT Pub. Nos. WO 91/06678; WO 04/018497 or WO07/123744; U.S. Pat. Nos. 7,057,026; 7,211,414; 7,315,019; 7,329,492 or7,405,281; or U.S. Pat. App. Pub. No. 2008/0108082, each of which isincorporated herein by reference. Arrays formed on flow cells used forcommercial sequencing platforms, such as those developed by Illumina(San Diego, Calif.), Life Technologies (a subsidiary of Thermo Fisher,Waltham Mass.), Pacific Biosciences (Menlo Park, Calif.), MGI (asubsidiary of BGI, Shenzhen, Guangdong, China), can also be useful.

A nucleic acid or other analyte can be attached to a support in a waythat provides detection at a single molecule level or at an ensemblelevel. For example, a plurality of different nucleic acids can beattached to a solid support in a way that an individual nucleic acidmolecule that is in a blocked or deblocked state on the support can bedistinguished from all neighboring nucleic acid molecules on thesupport. As such, one or more different templates can be attached to asolid support in a format where each single molecule template isphysically isolated and detected in a way that the single molecule isresolved from all other molecules on the solid support, for example, ina sequencing process set forth herein.

Alternatively, a composition or method of the present disclosure canemploy one or more ensembles, an ensemble being a population of analytesof the same type such as a population of nucleic acids having a commontemplate sequence. Cluster methods can be used to attach one or morenucleic acid ensembles to a solid support. As such, an array can have aplurality of ensembles, each of the ensembles being referred to as acluster or array site in that format. Clusters can be formed usingmethods known in the art such as bridge amplification, emulsion PCR orother methods set forth herein. The nucleic acids in a cluster caninclude a reversibly terminated nucleotide, deblocked nucleotide orextendable nucleotide

A system of the present disclosure can be configured to use a flow cell.The flow cell can include a detection channel where an analyticalreaction of interest can be observed. The analytical reaction can occurin solution phase within the flow cell. Alternatively, an analyticalreaction can occur on a solid support within the detection channel. Forexample, a reagent solution can be flowed over a solid support that isattached to analytes of interest, such as nucleic acids, and a resultingreaction can be observed on the solid support. Nucleic acids that arepresent in a flow cell, whether surface attached or not, can include a3′ nucleotide that is reversibly terminated, deblocked or extendable. Aflow cell allows convenient fluidic manipulation by passing solutionsthrough an ingress opening, into the detection channel and out of theinterior via an egress opening. For example, the detection channel canhave an observation area or volume such as an optically transparentwindow through which optical signals can be observed, an electricalcontact through which electronic signals can be observed or the like. Aparticularly useful flow cell has a window that is transparent toexcitation radiation and emission radiation used for luminescencedetection. Exemplary flow cells that can be used herein are described,for example, in US Pat. App. Pub. No. 2010/0111768 A1, WO 05/065814 orUS Pat. App. Pub. No. 2012/0270305 A1, each of which is incorporatedherein by reference.

The present disclosure provides a method for sequencing a nucleic acid.The method can be carried out on a primed template nucleic acid in whichthe primer has a 3′ ONH₂ reversible terminator moiety that is reactedwith a deblocking reagent having nitrous acid (HONO), thereby convertingthe primer to an extendable primer having a 3′ hydroxyl moiety. In someconfigurations, the reversibly terminated primer can have the followingstructure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH;and Q is a nucleic acid primer.

Alternatively, a sequencing method can be carried out on a primedtemplate nucleic acid in which the primer has a 3′-O-oxime protectingmoiety that is removed by treatment with a reagent having the structureR2-ONH₂ or other reversible terminator and, thereby converting theprimer to a reversibly terminated primer which can then be converted toan extendable primer having a 3′ hydroxyl moiety by, for example,reaction with nitrous acid (HONO). Alternatively, a sequencing methodcan be carried out on a primed template nucleic acid in which the primerhas a 3′-O-oxime reversible terminator moiety that is deblocked bytreatment with a reagent having the structure R2-ONH₂ and with nitrousacid (HONO), thereby converting the primer to an extendable primerhaving a 3′ hydroxyl moiety. R2 can independently be alkyl, alkenyl,alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

In embodiments, R2 is —C(R6)(R7)(R8), —C(O)(R6), —P(O)(R6)(R7),—C(R6)(═C(R7)(R8)), —Si(R6)(R7)(R8), —S O2(R6), substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C5-C6), substituted orunsubstituted cycloalkenyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆), substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆),substituted or unsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3to 6 membered, or 5 to 6 membered), substituted or unsubstituted aryl(e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl), or substituted orunsubstituted heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9membered heteroaryl, or 5 to 6 membered heteroaryl).

In embodiments, R2 is —C(R6)(R7)(R8). In embodiments, R2 is —C(O)(R6).In embodiments, R2 is —P(O)(R6)(R7). In embodiments, R2 is—C(R6)(═C(R7)(R8)). In embodiments, R2 is —Si(R6)(R7)(R8). Inembodiments, R2 is —SO2(R6). In embodiments, R2 is substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments,R2 is substituted or unsubstituted cycloalkenyl (e.g., C₃-C₈, C₃-C₆, orC₅-C₆). In embodiments, R2 is substituted or unsubstituted cycloalkynyl(e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R2 is substituted orunsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered,or 5 to 6 membered). In embodiments, R2 is substituted or unsubstitutedaryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). In embodiments, R2 issubstituted or unsubstituted heteroaryl (e.g., 5 to 10 memberedheteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl).In embodiments, R2 is unsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, orC₅-C₆). In embodiments, R2 is unsubstituted cycloalkenyl (e.g., C₃-C₈,C₃-C₆, or C₅-C₆). In embodiments, R2 is unsubstituted cycloalkynyl(e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R2 is unsubstitutedheteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered, or 5 to 6membered). In embodiments, R2 is unsubstituted aryl (e.g., C₆-C₁₀ aryl,C₁₀ aryl, or phenyl). In embodiments, R2 is unsubstituted heteroaryl(e.g., 5 to 10 membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to6 membered heteroaryl). In embodiments, R2 is not unsubstituted methyl.In embodiments, R2 is not unsubstituted ethyl. In embodiments, R2 is notunsubstituted propyl.

R6, R7, and R8 are independently hydrogen, halogen, —CCl₃, —CBr₃, —CF₃,—CI₃, —CHCl₂, —CHBr₂, —CHF₂, —CHI₂, —CH₂Cl, —CH₂Br, —CH₂F, —CH₂I, —CN,—OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂,—ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂, —NHSO₂H, —NHC(O)H, —NHC(O)OH, —NHOH,—OCCl₃, —OCF₃, —OCBr₃, —OCI₃, —OCHCl₂, —OCHBr₂, —OCHI₂, —OCHF₂, —OCH₂Cl,—OCH₂Br, —OCH₂I, —OCH₂F, —SF₅, —N₃, substituted or unsubstituted alkyl(e.g., C₁-C₈ alkyl, C₁-C₆ alkyl, or C1-C4 alkyl), substituted orunsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆ alkenyl, or C2-C4alkenyl), substituted or unsubstituted alkynyl (e.g., C₂-C₈ alkynyl,C₂-C₆ alkynyl, or C₂-C₄ alkynyl), substituted or unsubstitutedheteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to 6 memberedheteroalkyl, or 2 to 4 membered heteroalkyl), substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆), substituted orunsubstituted cycloalkenyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆), substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆),substituted or unsubstituted aryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, orphenyl), substituted or unsubstituted heteroaryl (e.g., 5 to 10 memberedheteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl),substituted or unsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3to 6 membered, or 5 to 6 membered), substituted or unsubstitutedaralkyl, substituted or unsubstituted heteroaralkyl, or substituted orunsubstituted (heteroalicyclyl)alkyl. In embodiments, R6, R7, and R8 arenot all hydrogen. In embodiments, R2 is —C(R6)(R7)(R8) and R6, R7, andR8 are not all hydrogen.

In embodiments, R6 is independently hydrogen. In embodiments, R6 isindependently halogen. In embodiments, R6 is independently —CCl₃. Inembodiments, R6 is independently —CBr₃. In embodiments, R6 isindependently —CF₃. In embodiments, R6 is independently —CI₃. Inembodiments, R6 is independently —CHCl₂. In embodiments, R6 isindependently —CHBr₂. In embodiments, R6 is independently —CHF₂. Inembodiments, R6 is independently —CHI₂. In embodiments, R6 isindependently —CH₂Cl. In embodiments, R6 is independently —CH₂Br. Inembodiments, R6 is independently —CH₂F. In embodiments, R6 isindependently —CH₂I. In embodiments, R6 is independently —CN. Inembodiments, R6 is independently —OH. In embodiments, R6 isindependently —NH₂. In embodiments, R6 is independently —COOH. Inembodiments, R6 is independently —CONH₂. In embodiments, R6 isindependently —NO₂. In embodiments, R6 is independently —SH. Inembodiments, R6 is independently —SO₃H. In embodiments, R6 isindependently —SO₄H. In embodiments, R6 is independently —SO₂NH₂. Inembodiments, R6 is independently —NHNH₂. In embodiments, R6 isindependently —ONH₂. In embodiments, R6 is independently —NHC(O)NHNH₂.In embodiments, R6 is independently —NHC(O)NH₂. In embodiments, R6 isindependently —NHSO₂H. In embodiments, R6 is independently —NHC(O)H. Inembodiments, R6 is independently —NHC(O)OH. In embodiments, R6 isindependently —NHOH. In embodiments, R6 is independently —OCCl₃. Inembodiments, R6 is independently —OCF₃. In embodiments, R6 isindependently —OCBr₃. In embodiments, R6 is independently —OCI₃. Inembodiments, R6 is independently —OCHCl₂. In embodiments, R6 isindependently —OCHBr₂. In embodiments, R6 is independently —OCHI₂. Inembodiments, R6 is independently —OCHF₂. In embodiments, R6 isindependently —OCH₂Cl. In embodiments, R6 is independently —OCH₂Br. Inembodiments, R6 is independently —OCH₂I. In embodiments, R6 isindependently —OCH₂F. In embodiments, R6 is independently —SF₅. Inembodiments, R6 is independently —N₃. In embodiments, R6 isindependently substituted or unsubstituted alkyl (e.g., C₁-C₈ alkyl,C₁-C₆ alkyl, or C₁-C₄ alkyl). In embodiments, R6 is independentlysubstituted or unsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆alkenyl, or C₂-C₄ alkenyl). In embodiments, R6 is independentlysubstituted or unsubstituted alkynyl (e.g., C₂-C₈ alkynyl, C₂-C₆alkynyl, or C2-C4 alkynyl). In embodiments, R6 is independentlysubstituted or unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R6 is independently substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments,R6 is independently substituted or unsubstituted cycloalkenyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R6 is independently substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). Inembodiments, R6 is independently substituted or unsubstituted aryl(e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). In embodiments, R6 isindependently substituted or unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R6 is independently substituted orunsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered,or 5 to 6 membered). In embodiments, R6 is independently substituted orunsubstituted aralkyl. In embodiments, R6 is independently substitutedor unsubstituted heteroaralkyl. In embodiments, R6 is independentlysubstituted or unsubstituted (heteroalicyclyl)alkyl.

In embodiments, R6 is independently unsubstituted alkyl (e.g., C₁-C₈alkyl, C₁-C₆ alkyl, or C₁-C₄ alkyl). In embodiments, R6 is independentlyunsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆ alkenyl, or C₂-C₄alkenyl). In embodiments, R6 is independently unsubstituted alkynyl(e.g., C₂-C₈ alkynyl, C₂-C₆ alkynyl, or C2-C4 alkynyl). In embodiments,R6 is independently unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R6 is independently unsubstitutedcycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R6 isindependently unsubstituted cycloalkenyl (e.g., C₃-C₈, C3-C6, or C₅-C₆).In embodiments, R6 is independently unsubstituted cycloalkynyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R6 is independentlyunsubstituted aryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). Inembodiments, R6 is independently unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R6 is independently unsubstitutedheteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered, or 5 to 6membered). In embodiments, R6 is independently unsubstituted aralkyl. Inembodiments, R6 is independently unsubstituted heteroaralkyl. Inembodiments, R6 is independently unsubstituted (heteroalicyclyl)alkyl.

In embodiments, R7 is independently hydrogen. In embodiments, R7 isindependently halogen. In embodiments, R7 is independently —CCl₃. Inembodiments, R7 is independently —CBr₃. In embodiments, R7 isindependently —CF₃. In embodiments, R7 is independently —CI₃. Inembodiments, R7 is independently —CHCl₂. In embodiments, R7 isindependently —CHBr₂. In embodiments, R7 is independently —CHF₂. Inembodiments, R7 is independently —CHI₂. In embodiments, R7 isindependently —CH₂Cl. In embodiments, R7 is independently —CH₂Br. Inembodiments, R7 is independently —CH₂F. In embodiments, R7 isindependently —CH₂I. In embodiments, R7 is independently —CN. Inembodiments, R7 is independently —OH. In embodiments, R7 isindependently —NH₂. In embodiments, R7 is independently —COOH. Inembodiments, R7 is independently —CONH₂. In embodiments, R7 isindependently —NO₂. In embodiments, R7 is independently —SH. Inembodiments, R7 is independently —SO₃H. In embodiments, R7 isindependently —SO₄H. In embodiments, R7 is independently —SO₂NH₂. Inembodiments, R7 is independently —NHNH₂. In embodiments, R7 isindependently —ONH₂. In embodiments, R7 is independently —NHC(O)NHNH₂.In embodiments, R7 is independently —NHC(O)NH₂. In embodiments, R7 isindependently —NHSO₂H. In embodiments, R7 is independently —NHC(O)H. Inembodiments, R7 is independently —NHC(O)OH. In embodiments, R7 isindependently —NHOH. In embodiments, R7 is independently —OCCl₃. Inembodiments, R7 is independently —OCF₃. In embodiments, R7 isindependently —OCBr₃. In embodiments, R7 is independently —OCI₃. Inembodiments, R7 is independently —OCHCl₂. In embodiments, R7 isindependently —OCHBr₂. In embodiments, R7 is independently —OCHI₂. Inembodiments, R7 is independently —OCHF₂. In embodiments, R7 isindependently —OCH₂Cl. In embodiments, R7 is independently —OCH₂Br. Inembodiments, R7 is independently —OCH₂I. In embodiments, R7 isindependently —OCH₂F. In embodiments, R7 is independently —SF₅. Inembodiments, R7 is independently —N₃. In embodiments, R7 isindependently substituted or unsubstituted alkyl (e.g., C₁-C₈ alkyl,C₁-C₆ alkyl, or C₁-C₄ alkyl). In embodiments, R7 is independentlysubstituted or unsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆alkenyl, or C₂-C₄ alkenyl). In embodiments, R7 is independentlysubstituted or unsubstituted alkynyl (e.g., C₂-C₈ alkynyl, C₂-C₆alkynyl, or C2-C4 alkynyl). In embodiments, R7 is independentlysubstituted or unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R7 is independently substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments,R7 is independently substituted or unsubstituted cycloalkenyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R7 is independently substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). Inembodiments, R7 is independently substituted or unsubstituted aryl(e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). In embodiments, R7 isindependently substituted or unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R7 is independently substituted orunsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered,or 5 to 6 membered). In embodiments, R7 is independently substituted orunsubstituted aralkyl. In embodiments, R7 is independently substitutedor unsubstituted heteroaralkyl. In embodiments, R7 is independentlysubstituted or unsubstituted (heteroalicyclyl)alkyl.

In embodiments, R7 is independently unsubstituted alkyl (e.g., C₁-C₈alkyl, C₁-C₆ alkyl, or C₁-C₄ alkyl). In embodiments, R7 is independentlyunsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆ alkenyl, or C₂-C₄alkenyl). In embodiments, R7 is independently unsubstituted alkynyl(e.g., C₂-C₈ alkynyl, C₂-C₆ alkynyl, or C2-C4 alkynyl). In embodiments,R7 is independently unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R7 is independently unsubstitutedcycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R7 isindependently unsubstituted cycloalkenyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆).In embodiments, R7 is independently unsubstituted cycloalkynyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R7 is independentlyunsubstituted aryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). Inembodiments, R7 is independently unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R7 is independently unsubstitutedheteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered, or 5 to 6membered). In embodiments, R7 is independently unsubstituted aralkyl. Inembodiments, R7 is independently unsubstituted heteroaralkyl. Inembodiments, R7 is independently unsubstituted (heteroalicyclyl)alkyl.

In embodiments, R8 is independently hydrogen. In embodiments, R8 isindependently halogen. In embodiments, R8 is independently —CCl₃. Inembodiments, R8 is independently —CBr₃. In embodiments, R8 isindependently —CF₃. In embodiments, R8 is independently —CI₃. Inembodiments, R8 is independently —CHCl₂. In embodiments, R8 isindependently —CHBr₂. In embodiments, R8 is independently —CHF₂. Inembodiments, R8 is independently —CHI₂. In embodiments, R8 isindependently —CH₂Cl. In embodiments, R8 is independently —CH₂Br. Inembodiments, R8 is independently —CH₂F. In embodiments, R8 isindependently —CH₂I. In embodiments, R8 is independently —CN. Inembodiments, R8 is independently —OH. In embodiments, R8 isindependently —NH₂. In embodiments, R8 is independently —COOH. Inembodiments, R8 is independently —CONH₂. In embodiments, R8 isindependently —NO₂. In embodiments, R8 is independently —SH. Inembodiments, R8 is independently —SO₃H. In embodiments, R8 isindependently —SO₄H. In embodiments, R8 is independently —SO₂NH₂. Inembodiments, R8 is independently —NHNH₂. In embodiments, R8 isindependently —ONH₂. In embodiments, R8 is independently —NHC(O)NHNH₂.In embodiments, R8 is independently —NHC(O)NH₂. In embodiments, R8 isindependently —NHSO₂H. In embodiments, R8 is independently —NHC(O)H. Inembodiments, R8 is independently —NHC(O)OH. In embodiments, R8 isindependently —NHOH. In embodiments, R8 is independently —OCCl₃. Inembodiments, R8 is independently —OCF₃. In embodiments, R8 isindependently —OCBr₃. In embodiments, R8 is independently —OCI₃. Inembodiments, R8 is independently —OCHCl₂. In embodiments, R8 isindependently —OCHBr₂. In embodiments, R8 is independently —OCHI₂. Inembodiments, R8 is independently —OCHF₂. In embodiments, R8 isindependently —OCH₂Cl. In embodiments, R8 is independently —OCH₂Br. Inembodiments, R8 is independently —OCH₂I. In embodiments, R8 isindependently —OCH₂F. In embodiments, R8 is independently —SF₅. Inembodiments, R8 is independently —N₃. In embodiments, R8 isindependently substituted or unsubstituted alkyl (e.g., C₁-C₈ alkyl,C₁-C₆ alkyl, or C1-C4 alkyl). In embodiments, R8 is independentlysubstituted or unsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆alkenyl, or C₂-C₄ alkenyl). In embodiments, R8 is independentlysubstituted or unsubstituted alkynyl (e.g., C₂-C₈ alkynyl, C₂-C₆alkynyl, or C2-C4 alkynyl). In embodiments, R8 is independentlysubstituted or unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R8 is independently substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments,R8 is independently substituted or unsubstituted cycloalkenyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R8 is independently substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). Inembodiments, R8 is independently substituted or unsubstituted aryl(e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). In embodiments, R8 isindependently substituted or unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R8 is independently substituted orunsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered,or 5 to 6 membered). In embodiments, R8 is independently substituted orunsubstituted aralkyl. In embodiments, R8 is independently substitutedor unsubstituted heteroaralkyl. In embodiments, R8 is independentlysubstituted or unsubstituted (heteroalicyclyl)alkyl.

In embodiments, R8 is independently unsubstituted alkyl (e.g., C₁-C₈alkyl, C₁-C₆ alkyl, or C₁-C₄ alkyl). In embodiments, R8 is independentlyunsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆ alkenyl, or C₂-C₄alkenyl). In embodiments, R8 is independently unsubstituted alkynyl(e.g., C₂-C₈ alkynyl, C₂-C₆ alkynyl, or C2-C4 alkynyl). In embodiments,R8 is independently unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R8 is independently unsubstitutedcycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R8 isindependently unsubstituted cycloalkenyl (e.g., C₃-C₈, C3-C6, or C₅-C₆).In embodiments, R8 is independently unsubstituted cycloalkynyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R8 is independentlyunsubstituted aryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). Inembodiments, R8 is independently unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R8 is independently unsubstitutedheteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered, or 5 to 6membered). In embodiments, R8 is independently unsubstituted aralkyl. Inembodiments, R8 is independently unsubstituted heteroaralkyl. Inembodiments, R8 is independently unsubstituted (heteroalicyclyl)alkyl.

The deprotecting treatment can be carried out by reacting the 3′-O-oximereversible terminator moiety with R2-ONH₂ to produce 3′-ONH₂ reversibleterminator moiety and then treating the 3′-ONH₂ moiety with HONO toproduce a 3′ hydroxyl moiety. In some configurations, the protectedprimer can have the following structure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH;and Q is a nucleic acid primer. R3 and R4 can independently be H, CH₃,alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl,heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl,(heteroalicyclyl)alkyl, or an optionally substituted variant thereof.The deblocking treatment can be carried out by reacting the 3′-O-oximereversible terminator moiety with R2-ONH₂ to produce 3′-ONH₂ moiety andthen treating the 3′-ONH₂ moiety with HONO to produce a 3′ hydroxylmoiety. In some configurations, the reversibly terminated primer canhave the following structure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH;and Q is a nucleic acid primer. R3 and R4 can independently be H, CH₃,alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl,heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl,(heteroalicyclyl)alkyl, or an optionally substituted variant thereof.

In embodiments, R2 is —C(R6)(R7)(R8), —C(O)(R6), —P(O)(R6)(R7),—C(R6)(═C(R7)(R8)), —Si(R6)(R7)(R8), —S O2(R6), substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C5-C6), substituted orunsubstituted cycloalkenyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆), substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆),substituted or unsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3to 6 membered, or 5 to 6 membered), substituted or unsubstituted aryl(e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl), or substituted orunsubstituted heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9membered heteroaryl, or 5 to 6 membered heteroaryl).

In embodiments, R2 is —C(R6)(R7)(R8). In embodiments, R2 is —C(O)(R6).In embodiments, R2 is —P(O)(R6)(R7). In embodiments, R2 is—C(R6)(═C(R7)(R8)). In embodiments, R2 is —Si(R6)(R7)(R8). Inembodiments, R2 is —SO₂(R6). In embodiments, R2 is substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments,R2 is substituted or unsubstituted cycloalkenyl (e.g., C₃-C₈, C₃-C₆, orC₅-C₆). In embodiments, R2 is substituted or unsubstituted cycloalkynyl(e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R2 is substituted orunsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered,or 5 to 6 membered). In embodiments, R2 is substituted or unsubstitutedaryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). In embodiments, R2 issubstituted or unsubstituted heteroaryl (e.g., 5 to 10 memberedheteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl).In embodiments, R2 is unsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, orC₅-C₆). In embodiments, R2 is unsubstituted cycloalkenyl (e.g., C₃-C₈,C₃-C₆, or C₅-C₆). In embodiments, R2 is unsubstituted cycloalkynyl(e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R2 is unsubstitutedheteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered, or 5 to 6membered). In embodiments, R2 is unsubstituted aryl (e.g., C₆-C₁₀ aryl,C₁₀ aryl, or phenyl). In embodiments, R2 is unsubstituted heteroaryl(e.g., 5 to 10 membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to6 membered heteroaryl). In embodiments, R6, R7, and R8 are not allhydrogen. In embodiments, R2 is —C(R6)(R7)(R8) and R6, R7, and R8 arenot all hydrogen. In embodiments, R2 is not unsubstituted methyl. Inembodiments, R2 is not unsubstituted ethyl. In embodiments, R2 is notunsubstituted propyl.

R6, R7, and R8 are independently hydrogen, halogen, —CCl₃, —CBr₃, —CF₃,—CI₃, —CHCl₂, —CHBr₂, —CHF₂, —CHI₂, —CH₂Cl, —CH₂Br, —CH₂F, —CH₂I, —CN,—OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂,—ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂, —NHSO₂H, —NHC(O)H, —NHC(O)OH, —NHOH,—OCCl₃, —OCF₃, —OCBr₃, —OCI₃, —OCHCl₂, —OCHBr₂, —OCHI₂, —OCHF₂, —OCH₂Cl,—OCH₂Br, —OCH₂I, —OCH₂F, —SF₅, —N₃, substituted or unsubstituted alkyl(e.g., C₁-C₈ alkyl, C₁-C₆ alkyl, or C1-C4 alkyl), substituted orunsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆ alkenyl, or C2-C4alkenyl), substituted or unsubstituted alkynyl (e.g., C₂-C₈ alkynyl,C₂-C₆ alkynyl, or C₂-C₄ alkynyl), substituted or unsubstitutedheteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to 6 memberedheteroalkyl, or 2 to 4 membered heteroalkyl), substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆), substituted orunsubstituted cycloalkenyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆), substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆),substituted or unsubstituted aryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, orphenyl), substituted or unsubstituted heteroaryl (e.g., 5 to 10 memberedheteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl),substituted or unsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3to 6 membered, or 5 to 6 membered), substituted or unsubstitutedaralkyl, substituted or unsubstituted heteroaralkyl, or substituted orunsubstituted (heteroalicyclyl)alkyl.

In embodiments, R6 is independently hydrogen. In embodiments, R6 isindependently halogen. In embodiments, R6 is independently —CCl₃. Inembodiments, R6 is independently —CBr₃. In embodiments, R6 isindependently —CF₃. In embodiments, R6 is independently —CI₃. Inembodiments, R6 is independently —CHCl₂. In embodiments, R6 isindependently —CHBr₂. In embodiments, R6 is independently —CHF₂. Inembodiments, R6 is independently —CHI₂. In embodiments, R6 isindependently —CH₂Cl. In embodiments, R6 is independently —CH₂Br. Inembodiments, R6 is independently —CH₂F. In embodiments, R6 isindependently —CH₂I. In embodiments, R6 is independently —CN. Inembodiments, R6 is independently —OH. In embodiments, R6 isindependently —NH₂. In embodiments, R6 is independently —COOH. Inembodiments, R6 is independently —CONH₂. In embodiments, R6 isindependently —NO₂. In embodiments, R6 is independently —SH. Inembodiments, R6 is independently —SO₃H. In embodiments, R6 isindependently —SO₄H. In embodiments, R6 is independently —SO₂NH₂. Inembodiments, R6 is independently —NHNH₂. In embodiments, R6 isindependently —ONH₂. In embodiments, R6 is independently —NHC(O)NHNH₂.In embodiments, R6 is independently —NHC(O)NH₂. In embodiments, R6 isindependently —NHSO₂H. In embodiments, R6 is independently —NHC(O)H. Inembodiments, R6 is independently —NHC(O)OH. In embodiments, R6 isindependently —NHOH. In embodiments, R6 is independently —OCCl₃. Inembodiments, R6 is independently —OCF₃. In embodiments, R6 isindependently —OCBr₃. In embodiments, R6 is independently —OCI₃. Inembodiments, R6 is independently —OCHCl₂. In embodiments, R6 isindependently —OCHBr₂. In embodiments, R6 is independently —OCHI₂. Inembodiments, R6 is independently —OCHF₂. In embodiments, R6 isindependently —OCH₂Cl. In embodiments, R6 is independently —OCH₂Br. Inembodiments, R6 is independently —OCH₂I. In embodiments, R6 isindependently —OCH₂F. In embodiments, R6 is independently —SF₅. Inembodiments, R6 is independently —N₃. In embodiments, R6 isindependently substituted or unsubstituted alkyl (e.g., C₁-C₈ alkyl,C₁-C₆ alkyl, or C₁-C₄ alkyl). In embodiments, R6 is independentlysubstituted or unsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆alkenyl, or C₂-C₄ alkenyl). In embodiments, R6 is independentlysubstituted or unsubstituted alkynyl (e.g., C₂-C₈ alkynyl, C₂-C₆alkynyl, or C2-C4 alkynyl). In embodiments, R6 is independentlysubstituted or unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R6 is independently substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments,R6 is independently substituted or unsubstituted cycloalkenyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R6 is independently substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). Inembodiments, R6 is independently substituted or unsubstituted aryl(e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). In embodiments, R6 isindependently substituted or unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R6 is independently substituted orunsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered,or 5 to 6 membered). In embodiments, R6 is independently substituted orunsubstituted aralkyl. In embodiments, R6 is independently substitutedor unsubstituted heteroaralkyl. In embodiments, R6 is independentlysubstituted or unsubstituted (heteroalicyclyl)alkyl.

In embodiments, R6 is independently unsubstituted alkyl (e.g., C₁-C₈alkyl, C₁-C₆ alkyl, or C₁-C₄ alkyl). In embodiments, R6 is independentlyunsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆ alkenyl, or C₂-C₄alkenyl). In embodiments, R6 is independently unsubstituted alkynyl(e.g., C₂-C₈ alkynyl, C₂-C₆ alkynyl, or C2-C4 alkynyl). In embodiments,R6 is independently unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R6 is independently unsubstitutedcycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R6 isindependently unsubstituted cycloalkenyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆).In embodiments, R6 is independently unsubstituted cycloalkynyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R6 is independentlyunsubstituted aryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). Inembodiments, R6 is independently unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R6 is independently unsubstitutedheteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered, or 5 to 6membered). In embodiments, R6 is independently unsubstituted aralkyl. Inembodiments, R6 is independently unsubstituted heteroaralkyl. Inembodiments, R6 is independently unsubstituted (heteroalicyclyl)alkyl.

In embodiments, R7 is independently hydrogen. In embodiments, R7 isindependently halogen. In embodiments, R7 is independently —CCl₃. Inembodiments, R7 is independently —CBr₃. In embodiments, R7 isindependently —CF₃. In embodiments, R7 is independently —CI₃. Inembodiments, R7 is independently —CHCl₂. In embodiments, R7 isindependently —CHBr₂. In embodiments, R7 is independently —CHF₂. Inembodiments, R7 is independently —CHI₂. In embodiments, R7 isindependently —CH₂Cl. In embodiments, R7 is independently —CH₂Br. Inembodiments, R7 is independently —CH₂F. In embodiments, R7 isindependently —CH₂I. In embodiments, R7 is independently —CN. Inembodiments, R7 is independently —OH. In embodiments, R7 isindependently —NH₂. In embodiments, R7 is independently —COOH. Inembodiments, R7 is independently —CONH₂. In embodiments, R7 isindependently —NO₂. In embodiments, R7 is independently —SH. Inembodiments, R7 is independently —SO₃H. In embodiments, R7 isindependently —SO₄H. In embodiments, R7 is independently —SO₂NH₂. Inembodiments, R7 is independently —NHNH₂. In embodiments, R7 isindependently —ONH₂. In embodiments, R7 is independently —NHC(O)NHNH₂.In embodiments, R7 is independently —NHC(O)NH₂. In embodiments, R7 isindependently —NHSO₂H. In embodiments, R7 is independently —NHC(O)H. Inembodiments, R7 is independently —NHC(O)OH. In embodiments, R7 isindependently —NHOH. In embodiments, R7 is independently —OCCl₃. Inembodiments, R7 is independently —OCF₃. In embodiments, R7 isindependently —OCBr₃. In embodiments, R7 is independently —OCI₃. Inembodiments, R7 is independently —OCHCl₂. In embodiments, R7 isindependently —OCHBr₂. In embodiments, R7 is independently —OCHI₂. Inembodiments, R7 is independently —OCHF₂. In embodiments, R7 isindependently —OCH₂Cl. In embodiments, R7 is independently —OCH₂Br. Inembodiments, R7 is independently —OCH₂I. In embodiments, R7 isindependently —OCH₂F. In embodiments, R7 is independently —SF₅. Inembodiments, R7 is independently —N₃. In embodiments, R7 isindependently substituted or unsubstituted alkyl (e.g., C₁-C₈ alkyl,C₁-C₆ alkyl, or C1-C4 alkyl). In embodiments, R7 is independentlysubstituted or unsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆alkenyl, or C₂-C₄ alkenyl). In embodiments, R7 is independentlysubstituted or unsubstituted alkynyl (e.g., C₂-C₈ alkynyl, C₂-C₆alkynyl, or C2-C4 alkynyl). In embodiments, R7 is independentlysubstituted or unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R7 is independently substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments,R7 is independently substituted or unsubstituted cycloalkenyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R7 is independently substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). Inembodiments, R7 is independently substituted or unsubstituted aryl(e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). In embodiments, R7 isindependently substituted or unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R7 is independently substituted orunsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered,or 5 to 6 membered). In embodiments, R7 is independently substituted orunsubstituted aralkyl. In embodiments, R7 is independently substitutedor unsubstituted heteroaralkyl. In embodiments, R7 is independentlysubstituted or unsubstituted (heteroalicyclyl)alkyl.

In embodiments, R7 is independently unsubstituted alkyl (e.g., C₁-C₈alkyl, C₁-C₆ alkyl, or C₁-C₄ alkyl). In embodiments, R7 is independentlyunsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆ alkenyl, or C₂-C₄alkenyl). In embodiments, R7 is independently unsubstituted alkynyl(e.g., C₂-C₈ alkynyl, C₂-C₆ alkynyl, or C2-C4 alkynyl). In embodiments,R7 is independently unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R7 is independently unsubstitutedcycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R7 isindependently unsubstituted cycloalkenyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆).In embodiments, R7 is independently unsubstituted cycloalkynyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R7 is independentlyunsubstituted aryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). Inembodiments, R7 is independently unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R7 is independently unsubstitutedheteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered, or 5 to 6membered). In embodiments, R7 is independently unsubstituted aralkyl. Inembodiments, R7 is independently unsubstituted heteroaralkyl. Inembodiments, R7 is independently unsubstituted (heteroalicyclyl)alkyl.

In embodiments, R8 is independently hydrogen. In embodiments, R8 isindependently halogen. In embodiments, R8 is independently —CCl₃. Inembodiments, R8 is independently —CBr₃. In embodiments, R8 isindependently —CF₃. In embodiments, R8 is independently —CI₃. Inembodiments, R8 is independently —CHCl₂. In embodiments, R8 isindependently —CHBr₂. In embodiments, R8 is independently —CHF₂. Inembodiments, R8 is independently —CHI₂. In embodiments, R8 isindependently —CH₂Cl. In embodiments, R8 is independently —CH₂Br. Inembodiments, R8 is independently —CH₂F. In embodiments, R8 isindependently —CH₂I. In embodiments, R8 is independently —CN. Inembodiments, R8 is independently —OH. In embodiments, R8 isindependently —NH₂. In embodiments, R8 is independently —COOH. Inembodiments, R8 is independently —CONH₂. In embodiments, R8 isindependently —NO₂. In embodiments, R8 is independently —SH. Inembodiments, R8 is independently —SO₃H. In embodiments, R8 isindependently —SO₄H. In embodiments, R8 is independently —SO₂NH₂. Inembodiments, R8 is independently —NHNH₂. In embodiments, R8 isindependently —ONH₂. In embodiments, R8 is independently —NHC(O)NHNH₂.In embodiments, R8 is independently —NHC(O)NH₂. In embodiments, R8 isindependently —NHSO₂H. In embodiments, R8 is independently —NHC(O)H. Inembodiments, R8 is independently —NHC(O)OH. In embodiments, R8 isindependently —NHOH. In embodiments, R8 is independently —OCCl₃. Inembodiments, R8 is independently —OCF₃. In embodiments, R8 isindependently —OCBr₃. In embodiments, R8 is independently —OCI₃. Inembodiments, R8 is independently —OCHCl₂. In embodiments, R8 isindependently —OCHBr₂. In embodiments, R8 is independently —OCHI₂. Inembodiments, R8 is independently —OCHF₂. In embodiments, R8 isindependently —OCH₂Cl. In embodiments, R8 is independently —OCH₂Br. Inembodiments, R8 is independently —OCH₂I. In embodiments, R8 isindependently —OCH₂F. In embodiments, R8 is independently —SF₅. Inembodiments, R8 is independently —N₃. In embodiments, R8 isindependently substituted or unsubstituted alkyl (e.g., C₁-C₈ alkyl,C₁-C₆ alkyl, or C1-C4 alkyl). In embodiments, R8 is independentlysubstituted or unsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆alkenyl, or C₂-C₄ alkenyl). In embodiments, R8 is independentlysubstituted or unsubstituted alkynyl (e.g., C₂-C₈ alkynyl, C₂-C₆alkynyl, or C2-C4 alkynyl). In embodiments, R8 is independentlysubstituted or unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R8 is independently substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments,R8 is independently substituted or unsubstituted cycloalkenyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R8 is independently substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). Inembodiments, R8 is independently substituted or unsubstituted aryl(e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). In embodiments, R8 isindependently substituted or unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R8 is independently substituted orunsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered,or 5 to 6 membered). In embodiments, R8 is independently substituted orunsubstituted aralkyl. In embodiments, R8 is independently substitutedor unsubstituted heteroaralkyl. In embodiments, R8 is independentlysubstituted or unsubstituted (heteroalicyclyl)alkyl.

In embodiments, R8 is independently unsubstituted alkyl (e.g., C₁-C₈alkyl, C₁-C₆ alkyl, or C₁-C₄ alkyl). In embodiments, R8 is independentlyunsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆ alkenyl, or C₂-C₄alkenyl). In embodiments, R8 is independently unsubstituted alkynyl(e.g., C₂-C₈ alkynyl, C₂-C₆ alkynyl, or C2-C4 alkynyl). In embodiments,R8 is independently unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R8 is independently unsubstitutedcycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R8 isindependently unsubstituted cycloalkenyl (e.g., C₃-C₈, C3-C6, or C₅-C₆).In embodiments, R8 is independently unsubstituted cycloalkynyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R8 is independentlyunsubstituted aryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). Inembodiments, R8 is independently unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R8 is independently unsubstitutedheteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered, or 5 to 6membered). In embodiments, R8 is independently unsubstituted aralkyl. Inembodiments, R8 is independently unsubstituted heteroaralkyl. Inembodiments, R8 is independently unsubstituted (heteroalicyclyl)alkyl.

Sequencing is commonly carried out using a DNA template and DNA primer.Accordingly, the primer used in a sequencing process can have thefollowing structure:

wherein Base is a nucleobase, and wherein DNA is the deoxyribonucleicacid primer. It will be understood that RNA can be used in place of DNAfor a sequencing process. R3 and R4 can independently be H, CH₃, alkyl,alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl,heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl,(heteroalicyclyl)alkyl, or an optionally substituted variant thereof.

A sequencing method of the present disclosure can include an extensionstep, whereby a nucleotide is added to the 3′ end of a deblocked primer.The nucleotide is typically added via polymerase catalysis. Thenucleotide can include a reversible terminator moiety so that only asingle nucleotide is added to the primer in the extension step.Similarly, a sequencing method can include an extension step, whereby anoligonucleotide is added to the 3′ end of the deblocked primer. Theoligonucleotide is typically added via ligase catalysis. The nucleotideat the 3′ end of the oligonucleotide can include a reversible terminatormoiety so that only a single oligonucleotide is added to the primer inthe extension step. A reversibly terminated nucleotide oroligonucleotide can include an exogenous label or, alternatively, thereversibly terminated nucleotide or oligonucleotide can lack exogenouslabels. By way of example, the reversibly terminated nucleotide that isused for primer extension can have the structure:

and can be produced through deblocking of a nucleotide such as

wherein Base is the nucleobase. R3 and R4 can independently be H, CH₃,alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl,heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl,(heteroalicyclyl)alkyl, or an optionally substituted variant thereof.

In some sequencing processes, a nucleotide or oligonucleotide that isadded to a primer in an extension step can have an exogenous labelmoiety such that the exogenous label is attached to the extended primer.Labelling an extended primer can be useful for a sequencing by synthesismethod or sequencing by ligation method such as those set forth infurther detail in the description and cited references below. Inalternative sequencing processes the nucleotide or oligonucleotide thatis added in an extension step will lack exogenous label moieties suchthat the extended primer will not have an exogenous label. Non-labelledextended primers can be useful for a Sequencing By Synthesis™ methodsuch as those set forth in further detail in the description and citedreferences below.

The use of reversibly terminated nucleotides and deblocking methods setforth herein can beneficially facilitate cyclical techniques that employrepeated cycles of reagent delivery and product detection. Each cyclecan include one step or multiple steps. For example, each cycle caninclude all steps needed to detect signals that are indicative of asingle nucleotide position in a template nucleic acid. Such sequencingprocesses can be referred to as cyclical reversible terminator (CRT)techniques. Each cycle in a CRT technique can include steps for (i)adding a single reversibly terminated nucleotide (or single reversiblyterminated oligonucleotide) to increment a nascent primer to anucleotide position that is to be detected; (ii) detecting a nucleotideat the single nucleotide position or at an adjacent position, and (iii)deblocking the nascent primer to allow a return to step (i) to start asubsequent cycle.

A specific example of a useful CRT nucleic acid sequencing process is aSequencing By Binding™ (SBB™) reaction, for example, as described incommonly owned US Pat. App. Pub. Nos. 2017/0022553 A1; 2018/0044727 A1;2018/0187245 A1; or 2018/0208983 A1, each of which is incorporatedherein by reference. SBB™ methods for determining the sequence of atemplate nucleic acid molecule can optionally be based on formation of aternary complex (between polymerase, primed nucleic acid and nextcorrect nucleotide) under specified conditions. The method can includean examination phase followed by a nucleotide incorporation phase (alsoreferred to as an extension phase).

The examination phase of an SBB™ process can be carried out for at leastone template nucleic acid molecule that is hybridized to a primer. Theprimer can be reversibly terminated. The primed template can becontacted with a reaction mixture that includes a polymerase and atleast one nucleotide type. Interaction of polymerase and a nucleotidewith the primed template nucleic acid molecule(s) can be observed underconditions where the nucleotide is not covalently added to theprimer(s); and the next base in each template nucleic acid can beidentified using the observed interaction of the polymerase andnucleotide with the primed template nucleic acid molecule(s). Theinteraction between the primed template, polymerase and nucleotide canbe detected in a variety of schemes. For example, the nucleotide cancontain a detectable label. Nucleotides with different nucleobase typescan be distinguished by different labels, respectively. Each type ofnucleobase can have a distinguishable label with respect to other typesof nucleobases. Alternatively, some or all of the different nucleobasetypes can have the same label and the different nucleotide types can bedistinguished based on separate deliveries of the respective nucleotidetypes to the flow cell. In some embodiments, the polymerase can belabeled. Polymerases that are associated with different nucleobase typescan have unique labels that distinguish the type of nucleotide to whichthey are associated. Alternatively, polymerases can have similar labelsand the different nucleobase types can be distinguished based onseparate deliveries of different nucleotide types to the flow cell.

During the examination phase of an SBB™ process, discrimination betweencorrect and incorrect nucleotides can be facilitated by ternary complexstabilization. A variety of conditions and reagents can be useful. Forexample, the primer can contain a reversible terminator moiety such asthose set forth herein; and/or polymerase cofactors that are requiredfor extension, such as divalent metal ions, can be absent; and/orinhibitory divalent cations that inhibit polymerase-based primerextension can be present; and/or the polymerase that is present in theexamination phase can have a chemical modification and/or mutation thatinhibits primer extension; and/or the nucleotides can have chemicalmodifications that inhibit incorporation, such as 5′ modifications thatremove or alter the native triphosphate moiety. The examination phasecan include detection using apparatus and methods set forth herein. Onceexamination is complete, the SBB™ process can proceed to the next cycleby removing the polymerase and nucleotides used for examination andsubjecting the primed template nucleic acid to further cycles ofdeblocking, extension and examination.

Washes can be carried out between the various delivery steps of an SBB™process. Wash steps can be performed between any of a variety of stepsset forth herein. For example, a wash step can be useful for separatinga primed template nucleic acid from other reagents that were contactedwith the primed template nucleic acid under ternary complex stabilizingconditions during an SBB™ process. Such a wash can remove one or morereagents from interfering with examination of a mixture or fromcontaminating a second mixture that is to be formed on a substrate (orin a vessel) that had previously been in contact with the first mixture.For example, a primed template nucleic acid can be contacted with apolymerase and at least one nucleotide type to form a first mixtureunder ternary complex stabilizing conditions, and the first mixture canbe examined. Optionally, a wash can be carried out prior to examinationto remove reagents that are not participating in formation of astabilized ternary complex. Alternatively, or additionally, a wash canbe carried out after the examination step to remove one or morecomponent of the first mixture from the primed template nucleic acid.Then the primed template nucleic acid can be contacted with a polymeraseand at least one other nucleotide to form a second mixture under ternarycomplex stabilizing conditions, and the second mixture can be examinedfor ternary complex formation. As before, an optional wash can becarried out prior to the second examination to remove reagents that arenot participating in formation of a stabilized ternary complex.

Another useful CRT sequencing process is sequencing-by-synthesis (SBS).SBS generally involves the enzymatic extension of a nascent primerthrough the iterative addition of nucleotides against a template strandto which the primer is hybridized. Briefly, SBS can be initiated bycontacting target nucleic acids, attached to sites in a flow cell, withone or more labeled nucleotides, DNA polymerase, etc. Those sites wherea primer is extended using the target nucleic acid as template willincorporate a labeled nucleotide that can be detected. Optionally, thelabeled nucleotides can further include a reversible terminator such asany of those set forth herein. For example, a nucleotide analog having areversible terminator moiety can be added to a primer such thatsubsequent extension cannot occur until a deblocking reagent of thepresent disclosure is delivered to remove the moiety. Thus, forembodiments that use reversible termination, a deblocking reagent can bedelivered to the vessel (before or after detection occurs). Washes canbe carried out between the various delivery steps. The cycle can beperformed n times to extend the primer by n nucleotides, therebydetecting a sequence of length n. Exemplary SBS procedures, reagents anddetection components that can be readily modified to employ a reversibleterminator and deblocking reagent of the present disclosure aredescribed, for example, in Bentley et al., Nature 456:53-59 (2008), WO04/018497; WO 91/06678; WO 07/123744; U.S. Pat. Nos. 7,057,026;7,329,492; 7,211,414; 7,315,019 or 7,405,281, and US Pat. App. Pub. No.2008/0108082 A1, each of which is incorporated herein by reference. Alsouseful are SBS methods that are commercially available from Illumina,Inc. (San Diego, Calif.).

Sequencing-by-ligation reactions are also useful including, for example,those described in Shendure et al. Science 309:1728-1732 (2005); U.S.Pat. No. 5,599,675; or U.S. Pat. No. 5,750,341, each of which isincorporated herein by reference. Some embodiments can includesequencing-by-hybridization procedures as described, for example, inBains et al., Journal of Theoretical Biology 135 (3), 303-7 (1988);Drmanac et al., Nature Biotechnology 16, 54-58 (1998); Fodor et al.,Science 251 (4995), 767-773 (1995); or WO 1989/10977, each of which isincorporated herein by reference. In both sequencing-by-ligation andsequencing-by-hybridization procedures, primers that are hybridized tonucleic acid templates are subjected to repeated cycles of extension byoligonucleotide ligation. Typically, the oligonucleotides arefluorescently labeled and can be detected to determine the sequence ofthe template. The primers and oligonucleotides used in such processescan include reversible terminators set forth herein and they can bedeblocked using reagents set forth herein.

Steps for the above sequencing methods can be carried out cyclically.For example, examination and extension steps of an SBB™ method can berepeated such that in each cycle a single next correct nucleotide isexamined (i.e. the next correct nucleotide being a nucleotide thatcorrectly binds to the nucleotide in a template nucleic acid that islocated immediately 5′ of the base in the template that is hybridized tothe 3′-end of the hybridized primer) and, subsequently, a single nextcorrect nucleotide is added to the primer. Any number of cycles of asequencing method set forth herein can be carried out including, forexample, at least 1, 2, 10, 25, 50, 100, 150, 250, 500 or more cycles.Alternatively or additionally, no more than 500, 250, 150, 100, 50, 25,10, 2 or 1 cycles are carried out.

Any of a variety of polymerases can be used in a method set forthherein. Reference to a particular polymerase, such as those exemplifiedthroughout this disclosure, will be understood to include functionalvariants thereof unless indicated otherwise. Particularly usefulfunctions of a polymerase include formation of a ternary complex,extension of a primer to introduce a nucleotide (such as a reversibleterminated nucleotide), or catalysis of the polymerization of a nucleicacid strand using an existing nucleic acid as a template.

Polymerases can be classified based on structural homology such as theclassification of polymerases into families identified as A, B, C, D, X,Y, and RT. DNA Polymerases in Family A include, for example, T7 DNApolymerase, eukaryotic mitochondrial DNA Polymerase γ, E. coli DNA PolI, Thermus aquaticus Pol I, and Bacillus stearothermophilus Pol I. DNAPolymerases in Family B include, for example, eukaryotic DNA polymerasesα, δ, and ε; DNA polymerase ζ; T4 DNA polymerase; Phi29 DNA polymerase;and RB69 bacteriophage DNA polymerase. Family C includes, for example,the E. coli DNA Polymerase III alpha subunit. Family B archaeon DNApolymerases include, for example, Vent, Deep Vent, Pfu and 9°N (e.g.,Therminator™ DNA polymerase from New England BioLabs Inc.; Ipswich,Mass.) polymerases. Family D includes, for example, polymerases derivedfrom the Euryarchaeota subdomain of Archaea. DNA Polymerases in Family Xinclude, for example, eukaryotic polymerases Pol β, pol σ, Pol λ, andPol μ, and S. cerevisiae Pol4. DNA Polymerases in Family Y include, forexample, Pol η, Pol ι, Pol κ, E. coli Pol IV (DINB) and E. coli Pol V(UmuD′2C). The RT (reverse transcriptase) family of DNA polymerasesincludes, for example, retrovirus reverse transcriptases and eukaryotictelomerases. Exemplary RNA polymerases include, but are not limited to,viral RNA polymerases such as T7 RNA polymerase; Eukaryotic RNApolymerases such as RNA polymerase I, RNA polymerase II, RNA polymeraseIII, RNA polymerase IV, and RNA polymerase V; and Archaea RNApolymerase.

Further examples of useful DNA polymerases include bacterial DNApolymerases, eukaryotic DNA polymerases, archaeal DNA polymerases, viralDNA polymerases and phage DNA polymerases. Bacterial DNA polymerasesinclude E. coli DNA polymerases I, II and III, IV and V, the Klenowfragment of E. coli DNA polymerase, Clostridium stercorarium (Cst) DNApolymerase, Clostridium thermocellum (Cth) DNA polymerase and Sulfolobussolfataricus (Sso) DNA polymerase. Eukaryotic DNA polymerases includeDNA polymerases α, β, γ, δ, ϵ, η, ζ, λ, σ, μ, and k, as well as the Revlpolymerase (terminal deoxycytidyl transferase) and terminaldeoxynucleotidyl transferase (TdT). Viral DNA polymerases include T4 DNApolymerase, phi-29 DNA polymerase, GA-1, phi-29-like DNA polymerases,PZA DNA polymerase, phi-15 DNA polymerase, Cpl DNA polymerase, Cp7 DNApolymerase, T7 DNA polymerase, and T4 polymerase. Other useful DNApolymerases include thermostable and/or thermophilic DNA polymerasessuch as Thermus aquaticus (Taq) DNA polymerase, Thermus filiformis (Tfi)DNA polymerase, Thermococcus zilligi (Tzi) DNA polymerase, Thermusthermophilus (Tth) DNA polymerase, Thermus flavusu (Tfl) DNA polymerase,Pyrococcus woesei (Pwo) DNA polymerase, Pyrococcus furiosus (Pfu) DNApolymerase and Turbo Pfu DNA polymerase, Thermococcus litoralis (Tli)DNA polymerase, Pyrococcus sp. GB-D polymerase, Thermotoga maritima(Tma) DNA polymerase, Bacillus stearothermophilus (Bst) DNA polymerase,Pyrococcus Kodakaraensis (KOD) DNA polymerase, Pfx DNA polymerase,Thermococcus sp. JDF-3 (JDF-3) DNA polymerase, Thermococcus gorgonarius(Tgo) DNA polymerase, Thermococcus acidophilium DNA polymerase;Sulfolobus acidocaldarius DNA polymerase; Thermococcus sp. go N-7 DNApolymerase; Pyrodictium occultum DNA polymerase; Methanococcus voltaeDNA polymerase; Methanococcus thermoautotrophicum DNA polymerase;Methanococcus jannaschii DNA polymerase; Desulfurococcus strain TOK DNApolymerase (D. Tok Pol); Pyrococcus abyssi DNA polymerase; Pyrococcushorikoshii DNA polymerase; Pyrococcus islandicum DNA polymerase;Thermococcus fumicolans DNA polymerase; Aeropyrum pernix DNA polymerase;and the heterodimeric DNA polymerase DP1/DP2. Engineered and modifiedpolymerases also are useful in connection with the disclosed techniques.For example, modified versions of the extremely thermophilic marinearchaea Thermococcus species 9° N (e.g., Therminator™ DNA polymerasefrom New England BioLabs Inc.; Ipswich, Mass.) can be used.

Useful RNA polymerases include, but are not limited to, viral RNApolymerases such as T7 RNA polymerase, T3 polymerase, SP6 polymerase,and Kll polymerase; Eukaryotic RNA polymerases such as RNA polymerase I,RNA polymerase II, RNA polymerase III, RNA polymerase IV, and RNApolymerase V; and Archaea RNA polymerase.

Another useful type of polymerase is a reverse transcriptase. Exemplaryreverse transcriptases include, but are not limited to, HIV-1 reversetranscriptase from human immunodeficiency virus type 1 (PDB 1HMV), HIV-2reverse transcriptase from human immunodeficiency virus type 2, M-MLVreverse transcriptase from the Moloney murine leukemia virus, AMVreverse transcriptase from the avian myeloblastosis virus, andTelomerase reverse transcriptase that maintains the telomeres ofeukaryotic chromosomes.

A polymerase having an intrinsic 3′-5′ proofreading exonuclease activitycan be useful for some applications of the methods and systems set forthherein. For example, the 3′-5′ exonuclease activity can be used toremove a reversibly terminated nucleotide from the 3′ end of a primer.Polymerases that substantially lack 3′-5′ proofreading exonucleaseactivity are also useful in some configurations, for example, in mostsequencing systems and methods. Absence of exonuclease activity can be awild type characteristic or a characteristic imparted by a variant orengineered polymerase structure. For example, exo minus Klenow fragmentis a mutated version of Klenow fragment that lacks 3′-5′ proofreadingexonuclease activity. Klenow fragment and its exo minus variant can beuseful in a method or composition set forth herein.

Polymerases that may be used in a method or composition set forth hereininclude naturally occurring polymerases and modified variations thereof,including, but not limited to, mutants, recombinants, fusions, geneticmodifications, chemical modifications, synthetics, and analogs. Usefulpolymerases for ternary complex formation and detection are not limitedto polymerases that have the ability to catalyze a polymerizationreaction. Optionally, a useful polymerase will have the ability tocatalyze a polymerization reaction in at least one condition that is notused during formation or examination of a stabilized ternary complex.Exemplary polymerases that can be used to form a stabilized ternarycomplex include, for example, wild type and mutant polymerases set forthin US Pat. App. Pub. Nos. 2017/0314072 A1 or 2018/0155698 A1, or U.S.Pat. App. Ser. No. 62/732,510, each of which is incorporated herein byreference.

Polymerases that contain an exogenous label moiety (e.g., an exogenousluminophore), which can be used to detect the polymerase (e.g. during anSBB™ examination step), can be useful in some embodiments. Optionally,the exogenous label moiety can be chemically linked to the polymerase,for example, using a free sulfhydryl or a free amine moiety of thepolymerase. An exogenous label moiety can also be attached to apolymerase via protein fusion. Exemplary label moieties that can beattached via protein fusion include, for example, green fluorescentprotein (GFP), phycobiliprotein (e.g. phycocyanin and phycoerythrin) orwavelength-shifted variants of GFP or phycobiliprotein.

Also provided is a nucleic acid detection apparatus that includes afluid reagent delivery system, a detection system, and a flow cell,wherein the fluid reagent delivery system is configured to deliver afluid reagent to the flow cell, wherein the detection system isconfigured to detect a signal in the flow cell, wherein the flow cell isattached to a first molecule having the structure:

wherein Base is a nucleobase, wherein DNA is independently a singlestranded deoxyribonucleic acid or double stranded deoxyribonucleic acid,and wherein the fluid reagent comprises a second molecule comprising thestructure: R2-ONH₂, wherein R2, R3 and R4 is independently alkyl,alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl,heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl,(heteroalicyclyl)alkyl, or an optionally substituted variant thereof.

An apparatus of the present disclosure can be configured for detectionof luminescence or fluorescence. Accordingly, the apparatus can includea detection system having an optical excitation apparatus, such as alaser, LED or lamp, and a luminescence detector such as a camera (e.g.complementary metal oxide semiconductor (CMOS) camera or charge coupleddevice (CCD) camera). Examples of detection apparatus and componentsthereof that can be used in a system or method herein are described, forexample, in US Pat. App. Pub. No. 2010/0111768 A1 or U.S. Pat. Nos.7,329,860; 8,951,781 or 9,193,996, each of which is incorporated hereinby reference. Other detection apparatus include those commercialized fornucleic acid sequencing such as those provided by Illumina™, Inc. (e.g.HiSeq™, MiSeq™, NextSeq™, or NovaSeq™ systems), Life Technologies™ (e.g.ABI PRISM™, or SOLiD™ systems), Pacific Biosciences (e.g. systems usingSMRT™ Technology such as the Sequel™ or RS II™ systems), or Qiagen (e.g.Genereader™ system). Other useful detectors are described in U.S. Pat.Nos. 5,888,737; 6,175,002; 5,695,934; 6,140,489; or 5,863,722; or USPat. Pub. Nos. 2007/007991 A1, 2009/0247414 A1, or 2010/0111768; orWO2007/123744, each of which is incorporated herein by reference in itsentirety.

Although the compositions and methods of the present disclosure areillustrated in the context of optical detection in several exemplaryconfigurations herein, it will be understood that other detectionmodalities can be used in addition or instead. For example, the detectorcan be an electronic detector used for detection of protons orpyrophosphate (see, for example, US Pat. App. Pub. Nos. 2009/0026082 A1;2009/0127589 A1; 2010/0137143 A1; or 2010/0282617 A1, each of which isincorporated herein by reference in its entirety, or the Ion Torrent™systems commercially available from ThermoFisher, Waltham, Mass.) or asused in detection of nanopores such as those commercialized by OxfordNanopore™, Oxford UK (e.g. MinION™ or PromethION™ systems) or set forthin U.S. Pat. No. 7,001,792; Soni & Meller, Clin. Chem. 53, 1996-2001(2007); Healy, Nanomed. 2, 459-481 (2007); or Cockroft, et al. J. Am.Chem. Soc. 130, 818-820 (2008), each of which is incorporated herein byreference. A FET detector can be used such as one or more of thosedescribed in U.S. Pat. App. Ser. No. 62/767,712; US Pat. App. Pub. Nos.2017/0240962 A1, 2018/0051316 A1, 2018/0112265 A1, 2018/0155773 A1 or2018/0305727 A1; or U.S. Pat. Nos. 9,164,053, 9,829,456, 10,036,064, or10,125,391, each of which is incorporated herein by reference.

Other detection techniques that can be used in a method set forth hereininclude, for example, mass spectrometry which can be used to perceivemass; surface plasmon resonance which can be used to perceive binding toa surface; absorbance which can be used to perceive the wavelength ofthe energy a label absorbs; calorimetry which can be used to perceivechanges in temperature due to presence of a label; electricalconductance or impedance which can be used to perceive electricalproperties of a label, or other known analytic techniques.

A useful detection apparatus can include a fluid reagent deliverysystem. The fluid delivery system can include a reaction vessel (e.g.flow cell) that is configured to carry out chemical reactions set forthherein. The reaction vessel can also be configured to allow detection ofthe reactions or products of the reactions. The fluid delivery systemcan include reservoirs for storing reagents. The fluids from thereagents can be delivered to a reaction vessel (e.g. a flow cell) viathe fluid delivery system. Spent reagents and products or waste from areaction can be evacuated from the reaction vessel to a waste reservoir.

In particular configurations, a fluid reagent delivery system isconfigured to deliver a primer extension reagent to the flow cell,wherein the primer extension reagent comprises a polymerase and anucleotide having a 3′ ONH₂ moiety. For example, a nucleotide that isstored or delivered by a fluid reagent delivery system can have thefollowing structure:

wherein Base is a nucleobase. R3 and R4 can independently be H, CH₃,alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl,heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl,(heteroalicyclyl)alkyl, or an optionally substituted variant thereof.Other reagents set forth herein, for example, those that are useful fora CRT sequencing process can be stored or delivered via a fluid reagentdelivery system. For example, the fluid reagent delivery system can beconfigured to deliver a ternary complex formation reagent to a reactionvessel, wherein the ternary complex formation reagent includes apolymerase and a nucleotide that is the next correct nucleotide for aprimed template nucleic acid.

A detection apparatus of the present disclosure can include a programmodule configured to direct the apparatus to perform a nucleic acidsequencing process, wherein the nucleic acid sequencing processcomprises repeated deliveries of the fluid reagent to a reaction vesselvia a fluid reagent delivery system and repeated detection of thereaction vessel by the detection system. Control of apparatus componentscan utilize a general purpose processor, a Digital Signal Processor(DSP), an Application Specific Integrated Circuit (ASIC), a FieldProgrammable Gate Array (FPGA) or other programmable logic device,discrete gate or transistor logic, discrete hardware components, or anycombination thereof designed to perform the functions described herein.A general purpose processor may be a microprocessor, but in thealternative, the processor may be any conventional processor,controller, microcontroller, or state machine. A processor may also beimplemented as a combination of computing devices, e.g., a combinationof a DSP and a microprocessor, a plurality of microprocessors, one ormore microprocessors in conjunction with a DSP core, or any other suchconfiguration. The same or different processor that is used to controlfluids can interact with the system to acquire, store and processsignals (e.g. signals detected in a method set forth herein). Inparticular embodiments, a processor can be used to determine, from thesignals, the identity of the nucleotide that is present at a particularlocation in a template nucleic acid. In some cases, the processor willidentify a sequence of nucleotides for the template from the signalsthat are detected.

A useful processor can include one or more of a personal computersystem, server computer system, thin client, thick client, hand-held orlaptop device, multiprocessor system, microprocessor-based system, settop box, programmable consumer electronic, network PC, minicomputersystem, mainframe computer system, smart phone, and distributed cloudcomputing environments that include any of the above systems or devices,and the like. The processor can include one or more processors orprocessing units, a memory architecture that may include RAM andnon-volatile memory. The memory architecture may further includeremovable/non-removable, volatile/non-volatile computer system storagemedia. Further, the memory architecture may include one or more readersfor reading from and writing to a non-removable, non-volatile magneticmedia, such as a hard drive, a magnetic disk drive for reading from andwriting to a removable, non-volatile magnetic disk, and/or an opticaldisk drive for reading from or writing to a removable, non-volatileoptical disk such as a CD-ROM or DVD-ROM. The processor may also includea variety of computer system readable media. Such media may be anyavailable media that is accessible by a cloud computing environment,such as volatile and non-volatile media, and removable and non-removablemedia.

The memory architecture may include at least one program product havingat least one program module implemented as executable instructions thatare configured to carry out one or more steps of a method set forthherein. For example, executable instructions may include an operatingsystem, one or more application programs, other program modules, andprogram data. Generally, program modules may include routines, programs,objects, components, logic, data structures, and so on, that performparticular tasks set forth herein.

The components of a processor or other programmable device may becoupled by an internal bus that may be implemented as one or more of anyof several types of bus structures, including a memory bus or memorycontroller, a peripheral bus, an accelerated graphics port, and aprocessor or local bus using any of a variety of bus architectures. Byway of example, and not limitation, such architectures include IndustryStandard Architecture (ISA) bus, Micro Channel Architecture (MCA) bus,Enhanced ISA (EISA) bus, Video Electronics Standards Association (VESA)local bus, and Peripheral Component Interconnects (PCI) bus.

A processor can optionally communicate with one or more external devicessuch as a keyboard, a pointing device (e.g. a mouse), a display, such asa graphical user interface (GUI), or other device that facilitatesinteraction of a user with a system of the present disclosure.Similarly, the processor can communicate with other devices (e.g., vianetwork card, modem, etc.). Such communication can occur via I/Ointerfaces. Still yet, a processor of a system herein may communicatewith one or more networks such as a local area network (LAN), a generalwide area network (WAN), and/or a public network (e.g., the Internet)via a suitable network adapter.

This disclosure further provides kits that can be used, for example, forcharacterizing nucleic acids. A kit can include reagents for carryingout one or more of the methods set forth herein or using or generating acomposition disclosed herein. For example, a kit can include one or morereagents set forth herein for deblocking a reversibly terminatednucleotide or nucleic acid. Alternatively or additionally, a kit of thepresent disclosure can include one or more reagents for carrying out aprimer extension step including, for example, a reversibly terminatednucleotide or reversibly terminated nucleic acid, and/or polymerase. Apolymerase that is used for an extension step or for an examination stepcan also be included in a kit. A kit of the invention can optionallyinclude reagents for carrying out other steps of a sequencing processincluding, for example, an examination steps used to create and detect astabilized ternary complex, a wash step, a step for producing nucleicacid clusters or the like.

Accordingly, the present disclosure provides a kit that includes a firstvessel containing a nucleotide comprising a 3′-O-oxime moiety and asecond vessel containing a reagent comprising the structure R2-ONH₂,wherein R2 is independently alkyl, alkenyl, alkynyl, cycloalkyl,cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl,heteroaralkyl, (heteroalicyclyl)alkyl, or an optionally substitutedvariant thereof.

In embodiments, R2 is —C(R6)(R7)(R8), —C(O)(R6), —P(O)(R6)(R7),—C(R6)(═C(R7)(R8)), —Si(R6)(R7)(R8), —S O₂(R6), substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C5-C6), substituted orunsubstituted cycloalkenyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆), substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆),substituted or unsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3to 6 membered, or 5 to 6 membered), substituted or unsubstituted aryl(e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl), or substituted orunsubstituted heteroaryl (e.g., 5 to 10 membered heteroaryl, 5 to 9membered heteroaryl, or 5 to 6 membered heteroaryl).

In embodiments, R2 is —C(R6)(R7)(R8). In embodiments, R2 is —C(O)(R6).In embodiments, R2 is —P(O)(R6)(R7). In embodiments, R2 is—C(R6)(═C(R7)(R8)). In embodiments, R2 is —Si(R6)(R7)(R8). Inembodiments, R2 is —SO₂(R6). In embodiments, R2 is substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments,R2 is substituted or unsubstituted cycloalkenyl (e.g., C₃-C₈, C₃-C₆, orC₅-C₆). In embodiments, R2 is substituted or unsubstituted cycloalkynyl(e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R2 is substituted orunsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered,or 5 to 6 membered). In embodiments, R2 is substituted or unsubstitutedaryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). In embodiments, R2 issubstituted or unsubstituted heteroaryl (e.g., 5 to 10 memberedheteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl).In embodiments, R2 is unsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, orC₅-C₆). In embodiments, R2 is unsubstituted cycloalkenyl (e.g., C₃-C₈,C₃-C₆, or C₅-C₆). In embodiments, R2 is unsubstituted cycloalkynyl(e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R2 is unsubstitutedheteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered, or 5 to 6membered). In embodiments, R2 is unsubstituted aryl (e.g., C₆-C₁₀ aryl,C₁₀ aryl, or phenyl). In embodiments, R2 is unsubstituted heteroaryl(e.g., 5 to 10 membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to6 membered heteroaryl). In embodiments, R2 is not unsubstituted methyl.In embodiments, R2 is not unsubstituted ethyl. In embodiments, R2 is notunsubstituted propyl.

R6, R7, and R8 are independently hydrogen, halogen, —CCl₃, —CBr₃, —CF₃,—CI₃, —CHCl₂, —CHBr₂, —CHF₂, —CHI₂, —CH₂Cl, —CH₂Br, —CH₂F, —CH₂I, —CN,—OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂,—ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂, —NHSO₂H, —NHC(O)H, —NHC(O)OH, —NHOH,—OCCl₃, —OCF₃, —OCBr₃, —OCI₃, —OCHCl₂, —OCHBr₂, —OCHI₂, —OCHF₂, —OCH₂Cl,—OCH₂Br, —OCH₂I, —OCH₂F, —SF₅, —N₃, substituted or unsubstituted alkyl(e.g., C₁-C₈ alkyl, C₁-C₆ alkyl, or C1-C4 alkyl), substituted orunsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆ alkenyl, or C2-C4alkenyl), substituted or unsubstituted alkynyl (e.g., C₂-C₈ alkynyl,C₂-C₆ alkynyl, or C₂-C₄ alkynyl), substituted or unsubstitutedheteroalkyl (e.g., 2 to 8 membered heteroalkyl, 2 to 6 memberedheteroalkyl, or 2 to 4 membered heteroalkyl), substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆), substituted orunsubstituted cycloalkenyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆), substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆),substituted or unsubstituted aryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, orphenyl), substituted or unsubstituted heteroaryl (e.g., 5 to 10 memberedheteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 membered heteroaryl),substituted or unsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3to 6 membered, or 5 to 6 membered), substituted or unsubstitutedaralkyl, substituted or unsubstituted heteroaralkyl, or substituted orunsubstituted (heteroalicyclyl)alkyl. In embodiments, R6, R7, and R8 arenot all hydrogen. In embodiments, R2 is —C(R6)(R7)(R8) and R6, R7, andR8 are not all hydrogen.

In embodiments, R6 is independently hydrogen. In embodiments, R6 isindependently halogen. In embodiments, R6 is independently —CCl₃. Inembodiments, R6 is independently —CBr₃. In embodiments, R6 isindependently —CF₃. In embodiments, R6 is independently —CI₃. Inembodiments, R6 is independently —CHCl₂. In embodiments, R6 isindependently —CHBr₂. In embodiments, R6 is independently —CHF₂. Inembodiments, R6 is independently —CHI₂. In embodiments, R6 isindependently —CH₂Cl. In embodiments, R6 is independently —CH₂Br. Inembodiments, R6 is independently —CH₂F. In embodiments, R6 isindependently —CH₂I. In embodiments, R6 is independently —CN. Inembodiments, R6 is independently —OH. In embodiments, R6 isindependently —NH₂. In embodiments, R6 is independently —COOH. Inembodiments, R6 is independently —CONH₂. In embodiments, R6 isindependently —NO₂. In embodiments, R6 is independently —SH. Inembodiments, R6 is independently —SO₃H. In embodiments, R6 isindependently —SO₄H. In embodiments, R6 is independently —SO₂NH₂. Inembodiments, R6 is independently —NHNH₂. In embodiments, R6 isindependently —ONH₂. In embodiments, R6 is independently —NHC(O)NHNH₂.In embodiments, R6 is independently —NHC(O)NH₂. In embodiments, R6 isindependently —NHSO₂H. In embodiments, R6 is independently —NHC(O)H. Inembodiments, R6 is independently —NHC(O)OH. In embodiments, R6 isindependently —NHOH. In embodiments, R6 is independently —OCCl₃. Inembodiments, R6 is independently —OCF₃. In embodiments, R6 isindependently —OCBr₃. In embodiments, R6 is independently —OCI₃. Inembodiments, R6 is independently —OCHCl₂. In embodiments, R6 isindependently —OCHBr₂. In embodiments, R6 is independently —OCHI₂. Inembodiments, R6 is independently —OCHF₂. In embodiments, R6 isindependently —OCH₂Cl. In embodiments, R6 is independently —OCH₂Br. Inembodiments, R6 is independently —OCH₂I. In embodiments, R6 isindependently —OCH₂F. In embodiments, R6 is independently —SF₅. Inembodiments, R6 is independently —N₃. In embodiments, R6 isindependently substituted or unsubstituted alkyl (e.g., C₁-C₈ alkyl,C₁-C₆ alkyl, or C₁-C₄ alkyl). In embodiments, R6 is independentlysubstituted or unsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆alkenyl, or C₂-C₄ alkenyl). In embodiments, R6 is independentlysubstituted or unsubstituted alkynyl (e.g., C₂-C₈ alkynyl, C₂-C₆alkynyl, or C₂-C₄ alkynyl). In embodiments, R6 is independentlysubstituted or unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R6 is independently substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments,R6 is independently substituted or unsubstituted cycloalkenyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R6 is independently substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). Inembodiments, R6 is independently substituted or unsubstituted aryl(e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). In embodiments, R6 isindependently substituted or unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R6 is independently substituted orunsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered,or 5 to 6 membered). In embodiments, R6 is independently substituted orunsubstituted aralkyl. In embodiments, R6 is independently substitutedor unsubstituted heteroaralkyl. In embodiments, R6 is independentlysubstituted or unsubstituted (heteroalicyclyl)alkyl.

In embodiments, R6 is independently unsubstituted alkyl (e.g., C₁-C₈alkyl, C₁-C₆ alkyl, or C₁-C₄ alkyl). In embodiments, R6 is independentlyunsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆ alkenyl, or C₂-C₄alkenyl). In embodiments, R6 is independently unsubstituted alkynyl(e.g., C₂-C₈ alkyl, C₂-C₆ alkyl, or C₂-C₄ alkyl). In embodiments, R6 isindependently unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R6 is independently unsubstitutedcycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R6 isindependently unsubstituted cycloalkenyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆).In embodiments, R6 is independently unsubstituted cycloalkynyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R6 is independentlyunsubstituted aryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). Inembodiments, R6 is independently unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R6 is independently unsubstitutedheteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered, or 5 to 6membered). In embodiments, R6 is independently unsubstituted aralkyl. Inembodiments, R6 is independently unsubstituted heteroaralkyl. Inembodiments, R6 is independently unsubstituted (heteroalicyclyl)alkyl.

In embodiments, R7 is independently hydrogen. In embodiments, R7 isindependently halogen. In embodiments, R7 is independently —CCl₃. Inembodiments, R7 is independently —CBr₃. In embodiments, R7 isindependently —CF₃. In embodiments, R7 is independently —CI₃. Inembodiments, R7 is independently —CHCl₂. In embodiments, R7 isindependently —CHBr₂. In embodiments, R7 is independently —CHF₂. Inembodiments, R7 is independently —CHI₂. In embodiments, R7 isindependently —CH₂Cl. In embodiments, R7 is independently —CH₂Br. Inembodiments, R7 is independently —CH₂F. In embodiments, R7 isindependently —CH₂I. In embodiments, R7 is independently —CN. Inembodiments, R7 is independently —OH. In embodiments, R7 isindependently —NH₂. In embodiments, R7 is independently —COOH. Inembodiments, R7 is independently —CONH₂. In embodiments, R7 isindependently —NO₂. In embodiments, R7 is independently —SH. Inembodiments, R7 is independently —SO₃H. In embodiments, R7 isindependently —SO₄H. In embodiments, R7 is independently —SO₂NH₂. Inembodiments, R7 is independently —NHNH₂. In embodiments, R7 isindependently —ONH₂. In embodiments, R7 is independently —NHC(O)NHNH₂.In embodiments, R7 is independently —NHC(O)NH₂. In embodiments, R7 isindependently —NHSO₂H. In embodiments, R7 is independently —NHC(O)H. Inembodiments, R7 is independently —NHC(O)OH. In embodiments, R7 isindependently —NHOH. In embodiments, R7 is independently —OCCl₃. Inembodiments, R7 is independently —OCF₃. In embodiments, R7 isindependently —OCBr₃. In embodiments, R7 is independently —OCI₃. Inembodiments, R7 is independently —OCHCl₂. In embodiments, R7 isindependently —OCHBr₂. In embodiments, R7 is independently —OCHI₂. Inembodiments, R7 is independently —OCHF₂. In embodiments, R7 isindependently —OCH₂Cl. In embodiments, R7 is independently —OCH₂Br. Inembodiments, R7 is independently —OCH₂I. In embodiments, R7 isindependently —OCH₂F. In embodiments, R7 is independently —SF₅. Inembodiments, R7 is independently —N₃. In embodiments, R7 isindependently substituted or unsubstituted alkyl (e.g., C₁-C₈ alkyl,C₁-C₆ alkyl, or C1-C4 alkyl). In embodiments, R7 is independentlysubstituted or unsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆alkenyl, or C₂-C₄ alkenyl). In embodiments, R7 is independentlysubstituted or unsubstituted alkynyl (e.g., C₂-C₈ alkynyl, C₂-C₆alkynyl, or C2-C4 alkynyl). In embodiments, R7 is independentlysubstituted or unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R7 is independently substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments,R7 is independently substituted or unsubstituted cycloalkenyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R7 is independently substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). Inembodiments, R7 is independently substituted or unsubstituted aryl(e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). In embodiments, R7 isindependently substituted or unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R7 is independently substituted orunsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered,or 5 to 6 membered). In embodiments, R7 is independently substituted orunsubstituted aralkyl. In embodiments, R7 is independently substitutedor unsubstituted heteroaralkyl. In embodiments, R7 is independentlysubstituted or unsubstituted (heteroalicyclyl)alkyl.

In embodiments, R7 is independently unsubstituted alkyl (e.g., C₁-C₈alkyl, C₁-C₆ alkyl, or C₁-C₄ alkyl). In embodiments, R7 is independentlyunsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆ alkenyl, or C₂-C₄alkenyl). In embodiments, R7 is independently unsubstituted alkynyl(e.g., C₂-C₈ alkynyl, C₂-C₆ alkynyl, or C2-C4 alkynyl). In embodiments,R7 is independently unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R7 is independently unsubstitutedcycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R7 isindependently unsubstituted cycloalkenyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆).In embodiments, R7 is independently unsubstituted cycloalkynyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R7 is independentlyunsubstituted aryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). Inembodiments, R7 is independently unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R7 is independently unsubstitutedheteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered, or 5 to 6membered). In embodiments, R7 is independently unsubstituted aralkyl. Inembodiments, R7 is independently unsubstituted heteroaralkyl. Inembodiments, R7 is independently unsubstituted (heteroalicyclyl)alkyl.

In embodiments, R8 is independently hydrogen. In embodiments, R8 isindependently halogen. In embodiments, R8 is independently —CCl₃. Inembodiments, R8 is independently —CBr₃. In embodiments, R8 isindependently —CF₃. In embodiments, R8 is independently —CI₃. Inembodiments, R8 is independently —CHCl₂. In embodiments, R8 isindependently —CHBr₂. In embodiments, R8 is independently —CHF₂. Inembodiments, R8 is independently —CHI₂. In embodiments, R8 isindependently —CH₂Cl. In embodiments, R8 is independently —CH₂Br. Inembodiments, R8 is independently —CH₂F. In embodiments, R8 isindependently —CH₂I. In embodiments, R8 is independently —CN. Inembodiments, R8 is independently —OH. In embodiments, R8 isindependently —NH₂. In embodiments, R8 is independently —COOH. Inembodiments, R8 is independently —CONH₂. In embodiments, R8 isindependently —NO₂. In embodiments, R8 is independently —SH. Inembodiments, R8 is independently —SO₃H. In embodiments, R8 isindependently —SO₄H. In embodiments, R8 is independently —SO₂NH₂. Inembodiments, R8 is independently —NHNH₂. In embodiments, R8 isindependently —ONH₂. In embodiments, R8 is independently —NHC(O)NHNH₂.In embodiments, R8 is independently —NHC(O)NH₂. In embodiments, R8 isindependently —NHSO₂H. In embodiments, R8 is independently —NHC(O)H. Inembodiments, R8 is independently —NHC(O)OH. In embodiments, R8 isindependently —NHOH. In embodiments, R8 is independently —OCCl₃. Inembodiments, R8 is independently —OCF₃. In embodiments, R8 isindependently —OCBr₃. In embodiments, R8 is independently —OCI₃. Inembodiments, R8 is independently —OCHCl₂. In embodiments, R8 isindependently —OCHBr₂. In embodiments, R8 is independently —OCHI₂. Inembodiments, R8 is independently —OCHF₂. In embodiments, R8 isindependently —OCH₂Cl. In embodiments, R8 is independently —OCH₂Br. Inembodiments, R8 is independently —OCH₂I. In embodiments, R8 isindependently —OCH₂F. In embodiments, R8 is independently —SF₅. Inembodiments, R8 is independently —N₃. In embodiments, R8 isindependently substituted or unsubstituted alkyl (e.g., C₁-C₈ alkyl,C₁-C₆ alkyl, or C₁-C₄ alkyl). In embodiments, R8 is independentlysubstituted or unsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆alkenyl, or C₂-C₄ alkenyl). In embodiments, R8 is independentlysubstituted or unsubstituted alkynyl (e.g., C₂-C₈ alkynyl, C₂-C₆alkynyl, or C2-C4 alkynyl). In embodiments, R8 is independentlysubstituted or unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R8 is independently substituted orunsubstituted cycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments,R8 is independently substituted or unsubstituted cycloalkenyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R8 is independently substitutedor unsubstituted cycloalkynyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). Inembodiments, R8 is independently substituted or unsubstituted aryl(e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). In embodiments, R8 isindependently substituted or unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R8 is independently substituted orunsubstituted heteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered,or 5 to 6 membered). In embodiments, R8 is independently substituted orunsubstituted aralkyl. In embodiments, R8 is independently substitutedor unsubstituted heteroaralkyl. In embodiments, R8 is independentlysubstituted or unsubstituted (heteroalicyclyl)alkyl.

In embodiments, R8 is independently unsubstituted alkyl (e.g., C₁-C₈alkyl, C₁-C₆ alkyl, or C₁-C₄ alkyl). In embodiments, R8 is independentlyunsubstituted alkenyl (e.g., C₂-C₈ alkenyl, C₂-C₆ alkenyl, or C₂-C₄alkenyl). In embodiments, R8 is independently unsubstituted alkynyl(e.g., C₂-C₈ alkynyl, C₂-C₆ alkynyl, or C2-C4 alkynyl). In embodiments,R8 is independently unsubstituted heteroalkyl (e.g., 2 to 8 memberedheteroalkyl, 2 to 6 membered heteroalkyl, or 2 to 4 memberedheteroalkyl). In embodiments, R8 is independently unsubstitutedcycloalkyl (e.g., C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R8 isindependently unsubstituted cycloalkenyl (e.g., C₃-C₈, C3-C6, or C₅-C₆).In embodiments, R8 is independently unsubstituted cycloalkynyl (e.g.,C₃-C₈, C₃-C₆, or C₅-C₆). In embodiments, R8 is independentlyunsubstituted aryl (e.g., C₆-C₁₀ aryl, C₁₀ aryl, or phenyl). Inembodiments, R8 is independently unsubstituted heteroaryl (e.g., 5 to 10membered heteroaryl, 5 to 9 membered heteroaryl, or 5 to 6 memberedheteroaryl). In embodiments, R8 is independently unsubstitutedheteroalicyclyl (e.g., 3 to 8 membered, 3 to 6 membered, or 5 to 6membered). In embodiments, R8 is independently unsubstituted aralkyl. Inembodiments, R8 is independently unsubstituted heteroaralkyl. Inembodiments, R8 is independently unsubstituted (heteroalicyclyl)alkyl.

Optionally, the kit can include nitrous acid (HONO). For example, in athird vessel. In particular configurations, the nucleotide can have thestructure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 can independently be H, CH₃, alkyl, alkenyl,alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

In embodiments, Q is independently a single stranded deoxyribonucleicacid or double stranded deoxyribonucleic acid.

Any of the components or articles used in performing the methods setforth herein can be usefully packaged into a kit. For example, the kitscan be packed to include some, many or all of the components or articlesused in performing the methods set forth herein. Exemplary componentsinclude, for example, labeled nucleotides (e.g. extendible labelednucleotides); polymerases (labeled or unlabeled); nucleotides havingterminator moieties such as a —ONH₂ moiety (e.g. unlabeled, reversiblyterminated nucleotides); reagents such as N-alkoxyamine reagents setforth herein; and the like as set forth herein and in references citedherein. Any of such reagents can include, for example, some, many or allof the fluids, components and/or articles used for performing one ormore of the subsequent steps for analysis of a primed template nucleicacid. A kit need not include a primer or template nucleic acid. Rather,a user of the kit can provide a primed template nucleic acid which is tobe combined with components of the kit. Similarly, a kit can exclude oneor more of the components set forth herein (such as a flow cell or othervessel) and, optionally, such excluded components can be provided by anend user.

One or more ancillary reagents also can be included in a kit. Suchancillary reagents can include any of the reagents exemplified aboveand/or other types of reagents useful in performing the methods setforth herein. Instructions can further be included in a kit. Theinstructions can include, for example, procedures for making anycomponents used in the methods set forth herein, performing one or moresteps of any embodiment of the methods set forth herein and/orinstructions for performing any of the subsequent analysis stepsemploying a primed template nucleic acid. For example, a kit can includeinstructions for extending a primer with a reversibly terminatednucleotide or a reversibly terminated oligonucleotide, or instructionsfor deblocking a reversibly terminated nucleotide or primer.

Optionally a kit can include identifying information in the form of alabel that can be read by a human user. Labels that are machine readablesuch as bar codes, microchips or radio-frequency identification (RFID)tags can also be useful.

In particular embodiments, a kit includes a cartridge having reservoirsto contain the reagents and further having fluidic components fortransferring reagents from the reservoirs to a detection instrument. Forexample, the fluidic components can be configured to transfer reagentsto a flow cell where stabilized ternary complexes are detected. Thecartridge can be configured for non-permanent introduction to a nucleicacid analysis system such as a nucleic acid sequencing platform.Accordingly, the cartridge can be configured for installation with, andremoval from, a detection apparatus. An exemplary fluidic cartridge thatcan be included in a kit (or system) of the present disclosure isdescribed in US Pat. App. Pub. Nos. 2018/0280975 A1 or 2019/0055596 A1,each of which is incorporated herein by reference.

In an aspect is provided a method of adding a 3′-O—NH₂ moiety to anucleotide having a 3′ protecting group, including contacting anucleotide having a 3′ protecting group to a reagent including thestructure R2-O—NH₂, wherein R2 has a molecular weight of at least 24. Inembodiments, the nucleotide having a 3′ protecting group includes riboseor deoxyribose. In embodiments, the nucleotide having a 3′ protectinggroup includes ribose. In embodiments, the nucleotide having a 3′protecting group includes 2′ deoxyribose. In embodiments, the nucleotidehaving a 3′ protecting group includes phosphate. In embodiments, thenucleotide having a 3′ protecting group includes triphosphate. Inembodiments, the nucleotide having a 3′ protecting group includes thestructure:

wherein the nucleotide that includes the 3′-O—NH₂ moiety includes thestructure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

In embodiments, the 3′ blocking group includes 3′-O-Oxime. Inembodiments, the 3′ blocking group includes 3′-O-aldoxime. Inembodiments, the 3′ blocking group includes 3′-O-ketoxime.

In embodiments, the nucleotide having a 3′ protecting group includes thestructure:

wherein the nucleotide that includes the 3′-O—NH₂ moiety includes thestructure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

In embodiments, the method adds a 3′ ONH₂ in place of a 3′ protectinggroup to at least 94% of a population of nucleotides having a 3′protecting group in no more than 3 hours. In embodiments, the methodadds a 3′ ONH₂ in place of a 3′ protecting group to at least 96% of apopulation of nucleotides having a 3′ protecting group in no more than 3hours. In embodiments, the method adds a 3′ ONH₂ in place of a 3′protecting group to at least 98% of a population of nucleotides having a3′ protecting group in no more than 3 hours. In embodiments, the methodadds a 3′ ONH₂ in place of a 3′ protecting group to at least 98% of apopulation of nucleotides having a 3′ protecting group in no more than 1hour.

In embodiments, the nucleotide having a 3′ protecting group includescytosine, and wherein method degrades no more than 6% of cytosine basesfrom a population including a plurality of the nucleotide having a 3′protecting group including cytosine. In embodiments, the nucleotidehaving a 3′ protecting group includes cytosine, and wherein methoddegrades no more than 5% of cytosine bases from a population including aplurality of the nucleotide having a 3′ protecting group includingcytosine. In embodiments, the nucleotide having a 3′ protecting groupincludes cytosine, and wherein method degrades no more than 4% ofcytosine bases from a population including a plurality of the nucleotidehaving a 3′ protecting group including cytosine. In embodiments, thenucleotide having a 3′ protecting group includes cytosine, and whereinmethod degrades no more than 3% of cytosine bases from a populationincluding a plurality of the nucleotide having a 3′ protecting groupincluding cytosine. In embodiments, the nucleotide having a 3′protecting group includes cytosine, and wherein method degrades no morethan 2% of cytosine bases from a population including a plurality of thenucleotide having a 3′ protecting group including cytosine. Inembodiments, the nucleotide having a 3′ protecting group includescytosine, and wherein method degrades no more than 1% of cytosine basesfrom a population including a plurality of the nucleotide having a 3′protecting group including cytosine.

In an aspect is provided a method of making a 3′-blocked nucleotide, themethod including contacting a 3′-protected nucleotide with a reagenthaving the structure R2-O—NH₂, R2-O—NHCH₃, R2-O—NHCOCH₃, or R2-O—CH₂N₃wherein R2 has a molecular weight of at least 24 g/mol and therebymaking a 3′-blocked nucleotide from a 3′-protected nucleotide.

In embodiments, R2 has a molecular weight of at least 36. Inembodiments, R2 includes a fluorine nucleus. In embodiments, R2 includesat least two carbon nuclei. In embodiments, R2 includes a carbon-carbondouble bond. In embodiments, R2 includes a tertiary carbon. Inembodiments, R2 includes a tert-butyl moiety. In embodiments, R2includes a cyclic moiety. In embodiments, R2 includes a silicon nucleus.In embodiments, R2 includes a phenyl ring. In embodiments, R2 includes anitrogen nucleus. In embodiments, R2 includes an oxygen nucleus. Inembodiments, R2 includes a hydroxylate moiety.

In an aspect is provided a method of making a 3′-blocked nucleotide, themethod including contacting a 3′-protected nucleotide with a reagenthaving the structure R2-O—NH₂ or R2-O—CH₂N₃ wherein R2 has a molecularweight of at least 24 g/mol and thereby making a 3′-blocked nucleotidefrom a 3′-protected nucleotide.

In embodiments, the 3′-blocked nucleotide includes a blocking moietybonded directly to the ribose 3′ carbon of the nucleotide; and theblocking moiety is —ONH₂, —ONHCOCH₃, —ONHCH₃, —OCH₂N₃. In embodiments,the 3′-blocked nucleotide includes a blocking moiety bonded directly tothe ribose 3′ carbon of the nucleotide; and the blocking moiety is —ONH₂or —OCH₂N₃. In embodiments, the 3′-blocked nucleotide includes ablocking moiety bonded directly to the ribose 3′ carbon of thenucleotide; and the blocking moiety is —ONH₂.

In embodiments, the 3′-protected nucleotide comprises a protectingmoiety directly covalently bonded to the ribose 3′ carbon of thenucleotide; and the protecting moiety is a 3′-O-oxime moiety.

In embodiments, the —O-oxime moiety has the formula: —O—N═C(R3)(R4); andR3 and R4 are independently hydrogen, substituted or unsubstitutedalkyl, substituted or unsubstituted alkenyl, substituted orunsubstituted alkynyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedcycloalkenyl, substituted or unsubstituted cycloalkynyl, substituted orunsubstituted aryl, substituted or unsubstituted heteroaryl, substitutedor unsubstituted heteroalicyclyl, substituted or unsubstituted aralkyl,substituted or unsubstituted heteroaralkyl, or substituted orunsubstituted (heteroalicyclyl)alkyl.

In embodiments, the —O-oxime moiety has the formula: —O—N═C(R3)(R4); R3is hydrogen; and R4 is substituted or unsubstituted alkyl, substitutedor unsubstituted alkenyl, substituted or unsubstituted alkynyl,substituted or unsubstituted heteroalkyl, substituted or unsubstitutedcycloalkyl, substituted or unsubstituted cycloalkenyl, substituted orunsubstituted cycloalkynyl, substituted or unsubstituted aryl,substituted or unsubstituted heteroaryl, substituted or unsubstitutedheteroalicyclyl, substituted or unsubstituted aralkyl, substituted orunsubstituted heteroaralkyl, or substituted or unsubstituted(heteroalicyclyl)alkyl.

In embodiments, the —O-oxime moiety has the formula: —O—N═C(R3)(R4); andR3 and R4 are independently substituted or unsubstituted alkyl,substituted or unsubstituted alkenyl, substituted or unsubstitutedalkynyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl,substituted or unsubstituted cycloalkynyl, substituted or unsubstitutedaryl, substituted or unsubstituted heteroaryl, substituted orunsubstituted heteroalicyclyl, substituted or unsubstituted aralkyl,substituted or unsubstituted heteroaralkyl, or substituted orunsubstituted (heteroalicyclyl)alkyl.

In embodiments, the 3′-blocked nucleotide and the 3′-protectednucleotide include an adenine moiety or derivative thereof, guaninemoiety or derivative thereof, cytosine moiety or derivative thereof,thymine moiety or derivative thereof, or uracil moiety or derivativethereof. In embodiments, the adenine derivative moiety, guaninederivative moiety, cytosine derivative moiety, thymine derivativemoiety, and uracil derivative moiety include a detectable moiety.

In embodiments, the 3′-blocked nucleotide and the 3′-protectednucleotide include a monophosphate moiety or derivative thereof,diphosphate moiety or derivative thereof, triphosphate moiety orderivative thereof, or monovalent nucleic acid moiety or derivativethereof. In embodiments, the 3′-blocked nucleotide and the 3′-protectednucleotide include a monophosphate moiety, diphosphate moiety,triphosphate moiety, or monovalent nucleic acid moiety. In embodiments,the 3′-blocked nucleotide and the 3′-protected nucleotide comprise atriphosphate moiety. In embodiments, the 3′-blocked nucleotide and the3′-protected nucleotide comprise a monovalent nucleic acid moiety. Inembodiments, the 3′-blocked nucleotide and the 3′-protected nucleotidecomprise a ribose moiety. In embodiments, the 3′-blocked nucleotide andthe 3′-protected nucleotide comprise a 2′ deoxyribose moiety.

In embodiments, R2 has a molecular weight of 1000 g/mol or less. Inembodiments, R2 has a molecular weight of at least 36 g/mol. Inembodiments, R2 has a molecular weight of at least 57 g/mol.

In embodiments, R2 includes at least two carbon nuclei, a fluorinenucleus, carbon-carbon double bond, tertiary carbon, tert-butyl moiety,cyclic moiety, silicon nucleus, phenyl ring, nitrogen nucleus, oxygennucleus, or hydroxylate moiety.

In embodiments, R2 is substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted cycloalkenyl, substituted or unsubstitutedcycloalkynyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl, substituted or unsubstituted heteroalicyclyl,substituted or unsubstituted aralkyl, substituted or unsubstitutedheteroaralkyl, or substituted or unsubstituted (heteroalicyclyl)alkyl.In embodiments, R2 is not unsubstituted methyl. In embodiments, R2 isnot unsubstituted ethyl. In embodiments, R2 is not unsubstituted propyl.

In embodiments, R2 is —C(R6)(R7)(R8), —C(O)(R6), —P(O)(R6)(R7),—C(R6)(═C(R7)(R8)), —Si(R6)(R7)(R8), —S O₂(R6), substituted orunsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl,substituted or unsubstituted cycloalkynyl, substituted or unsubstitutedheteroalicyclyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl; and R6, R7, and R8 are independently hydrogen,halogen, —CCl₃, —CBr₃, —CF₃, —CI₃, —CHCl₂, —CHBr₂, —CHF₂, —CHI₂, —CH₂Cl,—CH₂Br, —CH₂F, —CH₂I, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₃H,—SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂, —NHSO₂H,—NHC(O)H, —NHC(O)OH, —NHOH, —OCCl₃, —OCF₃, —OCBr₃, —OCI₃, —OCHCl₂,—OCHBr₂, —OCHI₂, —OCHF₂, —OCH₂Cl, —OCH₂Br, —OCH₂I, —OCH₂F, —SF₅, —N₃,substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted cycloalkenyl, substituted or unsubstitutedcycloalkynyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl, substituted or unsubstituted heteroalicyclyl,substituted or unsubstituted aralkyl, substituted or unsubstitutedheteroaralkyl, or substituted or unsubstituted (heteroalicyclyl)alkyl.In embodiments, R2 is —C(R6)(R7)(R8) and R6, R7, and R8 are not allhydrogen.

In embodiments, R2 is —C(R6)(R7)(R8), —C(O)(R6), —P(O)(R6)(R7),—C(R6)(═C(R7)(R8)), —Si(R6)(R7)(R8), —S O₂(R6), unsubstituted 6 memberedheteroalicyclyl, unsubstituted phenyl, substituted or unsubstitutedheteroaryl; and R6, R7, and R8 are independently hydrogen, halogen,—CCl₃, —CBr₃, —CF₃, —CI₃, —CHCl₂, —CHBr₂, —CHF₂, —CHI₂, —CH₂Cl, —CH₂Br,—CH₂F, —CH₂I, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₃H, —SO₄H,—SO₂NH₂, —NHNH₂, —ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂, —NHSO₂H, —NHC(O)H,—NHC(O)OH, —NHOH, —OCCl₃, —OCF₃, —OCBr₃, —OCI₃, —OCHCl₂, —OCHBr₂,—OCHI₂, —OCHF₂, —OCH₂Cl, —OCH₂Br, —OCH₂I, —OCH₂F, —SF₅, —N₃, substitutedor unsubstituted alkyl, substituted or unsubstituted alkenyl,substituted or unsubstituted alkynyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted cycloalkenyl, substituted or unsubstituted cycloalkynyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, substituted or unsubstituted heteroalicyclyl, substituted orunsubstituted aralkyl, substituted or unsubstituted heteroaralkyl, orsubstituted or unsubstituted (heteroalicyclyl)alkyl. In embodiments, R6,R7, and R8 are not all hydrogen.

In embodiments, the reagent has the formula:

In embodiments, the reagent has the formula:

In embodiments, the 3′-protected nucleotide has the structure:

the 3′-blocked nucleotide has the structure:

B is a nucleobase; R1 is hydrogen, —OH, halogen, —OCH₃; Q isindependently a nucleic acid moiety, triphosphate moiety, diphosphatemoiety, or monophosphate moiety; R3 and R4 are independently hydrogen,substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted cycloalkenyl, substituted or unsubstitutedcycloalkynyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl, substituted or unsubstituted heteroalicyclyl,substituted or unsubstituted aralkyl, substituted or unsubstitutedheteroaralkyl, or substituted or unsubstituted (heteroalicyclyl)alkyl.

In embodiments, the method adds a 3′ ONH₂ in place of a 3′ protectinggroup to at least 94% of a population of nucleotides having a 3′protecting group in no more than 3 hours. In embodiments, the methodadds a 3′ ONH₂ in place of a 3′ protecting group to at least 98% of apopulation of nucleotides having a 3′ protecting group in no more than 1hour.

In embodiments, the nucleotide having a 3′ protecting group includescytosine, and wherein method degrades no more than 6% of cytosine basesfrom a population including a plurality of said nucleotide having a 3′protecting group including cytosine. In embodiments, the nucleotidehaving a 3′ protecting group includes cytosine, and wherein methoddegrades no more than 1% of cytosine bases from a population including aplurality of said nucleotide having a 3′ protecting group includingcytosine.

In embodiments, the method further includes making a first plurality of3′-blocked nucleotides, the method including contacting a secondplurality of 3′-protected nucleotides with a third plurality of thereagent and thereby making a first plurality of 3′-blocked nucleotidesfrom a second plurality of 3′-protected nucleotides. In embodiments, thefirst plurality of 3′-blocked nucleotides are made for 3 hours or less.In embodiments, the first plurality of 3′-blocked nucleotides are madefor 2 hours or less. In embodiments, the first plurality of 3′-blockednucleotides are made for 1 hour or less.

In embodiments, at least 94% of the first plurality of 3′-protectednucleotide is made into the second plurality of 3′-blocked nucleotides.In embodiments, at least 96% of the first plurality of 3′-protectednucleotide is made into the second plurality of 3′-blocked nucleotides.In embodiments, at least 98% of the first plurality of 3′-protectednucleotide is made into the second plurality of 3′-blocked nucleotides.

In embodiments, the first plurality of 3′-blocked nucleotides includes afourth plurality of 3′-blocked nucleotides including a cytosine; and 6%or less of the cytosines are chemically modified by the third pluralityof the reagent. In embodiments, the first plurality of 3′-blockednucleotides includes a fourth plurality of 3′-blocked nucleotidesincluding a cytosine; and 5% or less of the cytosines are chemicallymodified by the third plurality of the reagent. In embodiments, thefirst plurality of 3′-blocked nucleotides includes a fourth plurality of3′-blocked nucleotides including a cytosine; and 4% or less of thecytosines are chemically modified by the third plurality of the reagent.In embodiments, the first plurality of 3′-blocked nucleotides includes afourth plurality of 3′-blocked nucleotides including a cytosine; and 3%or less of the cytosines are chemically modified by the third pluralityof the reagent. In embodiments, the first plurality of 3′-blockednucleotides includes a fourth plurality of 3′-blocked nucleotidesincluding a cytosine; and 2% or less of the cytosines are chemicallymodified by the third plurality of the reagent. In embodiments, thefirst plurality of 3′-blocked nucleotides includes a fourth plurality of3′-blocked nucleotides including a cytosine; and 1% or less of thecytosines are chemically modified by the third plurality of the reagent.

In an aspect is provided a composition including a population ofcytosine nucleotides wherein at least 94% of the population of cytosinenucleotides include a 3′ —O—NH₂, wherein no more than 8% of thepopulation of cytosine nucleotides include a 3′ moiety other than—O—NH₂, and wherein no more than 6% of the population of cytosinenucleotides include a modified cytosine base.

In embodiments, at least 96% of the population of cytosine nucleotidesinclude a 3′-O—NH₂. In embodiments, at least 98% of the population ofcytosine nucleotides include a 3′-O—NH₂. In embodiments, at least 99% ofthe population of cytosine nucleotides include a 3′-O—NH₂.

In embodiments, no more than 6% of the population of cytosinenucleotides include a 3′ moiety other than —O—NH₂. In embodiments, nomore than 4% of the population of cytosine nucleotides include a 3′moiety other than —O—NH₂. In embodiments, no more than 2% of thepopulation of cytosine nucleotides include a 3′ moiety other than—O—NH₂. In embodiments, no more than 1% of the population of cytosinenucleotides include a 3′ moiety other than —O—NH₂.

In embodiments, no more than 4% of the population of cytosinenucleotides include a modified cytosine base. In embodiments, no morethan 2% of the population of cytosine nucleotides include a modifiedcytosine base. In embodiments, no more than 1% of the population ofcytosine nucleotides include a modified cytosine base.

In embodiments, at least 98% of the population of cytosine nucleotidesinclude a 3′-O—NH₂, wherein no more than 1% of the population ofcytosine nucleotides include a 3′ moiety other than —O—NH₂, and whereinno more than 1% of the population of cytosine nucleotides include amodified cytosine base.

In embodiments, the composition is an aqueous solution. In embodiments,the pH of the solution is no less than 4 and no greater than 8.

In embodiments, the composition includes a reagent including thestructure R2-O—NH₂. In embodiments, R2 includes a molecular weight of atleast 24, 26, 57, or 100. In embodiments, R2 includes a molecular weightof at least 24. In embodiments, R2 includes a molecular weight of atleast 36. In embodiments, R2 includes at least two carbon nuclei, afluorine nucleus, carbon-carbon double bond, tertiary carbon, tert-butylmoiety, cyclic moiety, silicon nucleus, phenyl ring, nitrogen nucleus,oxygen nucleus, or hydroxylate moiety. In embodiments, R2 includes atleast two carbon nuclei. In embodiments, R2 includes a fluorine nucleus.In embodiments, R2 includes a carbon-carbon double bond. In embodiments,R2 includes a tertiary carbon. In embodiments, R2 includes a tert-butylmoiety. In embodiments, R2 includes a cyclic moiety. In embodiments, R2includes a silicon nucleus. In embodiments, R2 includes a phenyl ring.In embodiments, R2 includes a nitrogen nucleus. In embodiments, R2includes a phenyl ring. In embodiments, R2 includes an oxygen nucleus.In embodiments, R2 includes a hydroxylated moiety.

In embodiments, the reagent including the structure R2-O—NH₂ is selectedfrom the group consisting of:

In embodiments, the reagent including the structure R2-O—NH₂ is selectedfrom the group consisting of:

In embodiments, the reagent including the structure R2-O—NH₂ is

In embodiments, the reagent including the structure R2-O—NH₂ is

In embodiments, the reagent including the structure R2-O—NH₂ is

In embodiments, the 3′ moiety other than —O—NH₂ includes a 3′ O-oxime.In embodiments, the 3′ moiety other than —O—NH₂ includes a 3′O-aldoxime. In embodiments, the 3′ moiety other than —O—NH₂ includes a3′ O-ketoxime.

In embodiments, the composition includes a reagent including thestructure R2-O—NHCH₃ or R2-O—CH₂N₃. In embodiments, the compositionincludes a reagent including the structure R2-O—NHCH₃. In embodiments,the composition includes a reagent including the structure R2-O—CH₂N₃.

In embodiments, at least some of the cytosine nucleotides having a 3′moiety other than —O—NH₂ nucleotide include the structure:

wherein B is a cytosine nucleobase; R1 is independently halogen, OCH₃, Hor OH, Q is independently monophosphate, diphosphate, triphosphate, ornucleic acid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl,alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

In an aspect is provided a method of formulating a sequencing reagent,including contacting a composition including a 3′ protected nucleotideto a reagent including a reversible terminator moiety to produce acomposition including a nucleotide including a reversible terminatormoiety, and formulating the composition including a nucleotide includinga reversible terminator moiety as a sequencing reagent, whereinformulating the composition including a reversible terminator moietydoes not include further purification of the composition including areversible terminator moiety.

In embodiments, the method further includes applying the sequencingreagent to a sequencing reagent to yield a sequencing run of at least100 bases having a quality score of at least Q30. In embodiments, thereagent including a reversible terminator moiety has a structureR2-O—NH₂.

In embodiments, R2 is selected from the group consisting of—C(R6)(R7)(R8), —C(O)(R6), —P(O)(R6)(R7), —C(R6)(═C(R7)(R8)),—Si(R6)(R7)(R8), —S O2(R6), substituted or unsubstituted cycloalkyl,substituted or unsubstituted cycloalkenyl, substituted or unsubstitutedcycloalkynyl, substituted or unsubstituted heteroalicyclyl, substitutedor unsubstituted aryl, substituted or unsubstituted heteroaryl; and R6,R7, and R8 are independently hydrogen, halogen, —CCl₃, —CBr₃, —CF₃,—CI₃, —CHCl₂, —CHBr₂, —CHF₂, —CHI₂, —CH₂Cl, —CH₂Br, —CH₂F, —CH₂I, —CN,—OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₃H, —SO₄H, —SO₂NH₂, —NHNH₂,—ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂, —NHSO₂H, —NHC(O)H, —NHC(O)OH, —NHOH,—OCCl₃, —OCF₃, —OCBr₃, —OCI₃, —OCHCl₂, —OCHBr₂, —OCHI₂, —OCHF₂, —OCH₂Cl,—OCH₂Br, —OCH₂I, —OCH₂F, —SF₅, —N₃, substituted or unsubstituted alkyl,substituted or unsubstituted alkenyl, substituted or unsubstitutedalkynyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl,substituted or unsubstituted cycloalkynyl, substituted or unsubstitutedaryl, substituted or unsubstituted heteroaryl, substituted orunsubstituted heteroalicyclyl, substituted or unsubstituted aralkyl,substituted or unsubstituted heteroaralkyl, or substituted orunsubstituted (heteroalicyclyl)alkyl. In embodiments, R2 is —C(CH₃)₃. Inembodiments, R2 is —C(R6)(R7)(R8) and R6, R7, and R8 are not allhydrogen.

In embodiments, R2 includes at least two carbon nuclei, a fluorinenucleus, carbon-carbon double bond, tertiary carbon, tert-butyl moiety,cyclic moiety, silicon nucleus, phenyl ring, nitrogen nucleus, oxygennucleus, or hydroxylate moiety. In embodiments, R2 includes at least twocarbon nuclei, carbon-carbon double bond, tertiary carbon, tert-butylmoiety, cyclic moiety, or phenyl ring. In embodiments, R2 includes atleast two carbon nuclei. In embodiments, R2 includes a fluorine nucleus,silicon nucleus, nitrogen nucleus, oxygen nucleus, or hydroxylatemoiety. In embodiments, R2 is —CH₂CH₃, —CH₂CHCH₂, or —C(CH₃)₃. Inembodiments, R2 is-C(CH₃)₃. In embodiments, R2 is not unsubstitutedmethyl. In embodiments, R2 is not unsubstituted ethyl. In embodiments,R2 is not unsubstituted propyl.

In embodiments, R2 has a molecular weight greater than 24, 36, 57, or100. In embodiments, R2 has a molecular weight of at least 24, 36, 57,100, 200, 300, 400, 500, 600, 700, 800, or 900. In embodiments, R2 has amolecular weight of at least 24. In embodiments, R2 has a molecularweight of at least 36. In embodiments, R2 has a molecular weight of atleast 57. In embodiments, R2 has a molecular weight of at least 100. Inembodiments, R2 has a molecular weight of at least 200. In embodiments,R2 has a molecular weight of at least 300. In embodiments, R2 has amolecular weight of at least 400. In embodiments, R2 has a molecularweight of at least 500. In embodiments, R2 has a molecular weight of atleast 600. In embodiments, R2 has a molecular weight of at least 700. Inembodiments, R2 has a molecular weight of at least 800. In embodiments,R2 has a molecular weight of at least 900.

In embodiments, the 3′ protected nucleotide includes a 3′-O-oximemoiety. In embodiments, the oxime is an aldoxime or ketoxime. Inembodiments, the oxime is an aldoxime. In embodiments, the oxime is aketoxime.

In embodiments, the composition including a nucleotide including areversible terminator moiety includes no more than 6% of the 3′protected nucleotide relative to 3′ protected nucleotide presentinitially. In embodiments, the composition including a nucleotideincluding a reversible terminator moiety includes no more than 5%, 4%,3%, 2%, or 1% of the 3′ protected nucleotide relative to 3′ protectednucleotide present initially. In embodiments, the composition includinga nucleotide including a reversible terminator moiety includes no morethan 5% of the 3′ protected nucleotide relative to 3′ protectednucleotide present initially. In embodiments, the composition includinga nucleotide including a reversible terminator moiety includes no morethan 4% of the 3′ protected nucleotide relative to 3′ protectednucleotide present initially. In embodiments, the composition includinga nucleotide including a reversible terminator moiety includes no morethan 3% of the 3′ protected nucleotide relative to 3′ protectednucleotide present initially. In embodiments, the composition includinga nucleotide including a reversible terminator moiety includes no morethan 2% of the 3′ protected nucleotide relative to 3′ protectednucleotide present initially. In embodiments, the composition includinga nucleotide including a reversible terminator moiety includes no morethan 1% of the 3′ protected nucleotide relative to 3′ protectednucleotide present initially.

In embodiments, the composition including a nucleotide including areversible terminator moiety includes degraded or modified dCnucleobases at a concentration of no more than 6% of total dCnucleobases in the composition including a nucleotide including areversible terminator moiety. In embodiments, the composition includinga nucleotide including a reversible terminator moiety includes degradedor modified dC nucleobases at a concentration of no more than 5%, 4%,3%, 2%, or 1% of total dC nucleobases in the composition including anucleotide including a reversible terminator moiety. In embodiments, thecomposition including a nucleotide including a reversible terminatormoiety includes degraded or modified dC nucleobases at a concentrationof no more than 5% of total dC nucleobases in the composition includinga nucleotide including a reversible terminator moiety. In embodiments,the composition including a nucleotide including a reversible terminatormoiety includes degraded or modified dC nucleobases at a concentrationof no more than 4% of total dC nucleobases in the composition includinga nucleotide including a reversible terminator moiety. In embodiments,the composition including a nucleotide including a reversible terminatormoiety includes degraded or modified dC nucleobases at a concentrationof no more than 3% of total dC nucleobases in the composition includinga nucleotide including a reversible terminator moiety. In embodiments,the composition including a nucleotide including a reversible terminatormoiety includes degraded or modified dC nucleobases at a concentrationof no more than 2% of total dC nucleobases in the composition includinga nucleotide including a reversible terminator moiety. In embodiments,the composition including a nucleotide including a reversible terminatormoiety includes degraded or modified dC nucleobases at a concentrationof no more than 1% of total dC nucleobases in the composition includinga nucleotide including a reversible terminator moiety.

In an aspect is provided a method for modifying a nucleotide, includingreacting a nucleotide including a 3′-O-oxime moiety with a reagentincluding the structure R2-O—NH₂ to produce a nucleotide including a3′-O—NH₂ moiety, wherein R2 is independently alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

In embodiments, the nucleotide that includes the 3′-O-oxime moietyincludes the structure:

wherein the nucleotide that includes the 3′-O—NH₂ moiety includes thestructure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

In embodiments, the nucleotide that is produced includes adeoxynucleotide. In embodiments, the nucleotide that is producedincludes:

wherein Base is the nucleobase, and wherein DNA is independently asingle stranded deoxyribonucleic acid or double strandeddeoxyribonucleic acid.

In embodiments, the nucleobase is a purine or pyrimidine. Inembodiments, the nucleobase is independently adenine, cytosine, guanine,thymine, or uracil. In embodiments, the nucleobase is independently5-methylcytosine, hypoxanthine, xanthine, inosine, isoguanine,isocytosine, or 7-deazaguanine.

In embodiments, the reagent is independently one of:

In embodiments, the reaction occurs in an aqueous solution. Inembodiments, the nucleotide is attached to a solid support in contactwith the aqueous solution. In embodiments, the reagent that includes thestructure R2-O—NH₂ is attached to a solid support in contact with theaqueous solution. In embodiments, the pH of the solution is no less than4 and no greater than 8.

In an aspect is provided a solution including a nucleotide including a3′-O-oxime moiety and a reagent including the structure R2-O—NH₂,wherein R2 is independently alkyl, alkenyl, alkynyl, cycloalkyl,cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl,heteroaralkyl, (heteroalicyclyl)alkyl, or an optionally substitutedvariant thereof. In embodiments, R2 is not unsubstituted methyl. Inembodiments, R2 is not unsubstituted ethyl. In embodiments, R2 is notunsubstituted propyl.

In embodiments, the nucleotide includes the structure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

In embodiments, the nucleobase is a purine or pyrimidine. Inembodiments, the nucleobase is independently adenine, cytosine, guanine,thymine, or uracil. In embodiments, the nucleobase is complementary toadenine, cytosine, guanine, thymine, or uracil. In embodiments, thenucleobase is independently 5-methylcytosine, hypoxanthine, xanthine,inosine, isoguanine, isocytosine, or 7-deazaguanine. In embodiments, thenucleobase includes an exogenous label moiety.

In embodiments, R1 is H. In embodiments, Q is deoxyribonucleic acid. Inembodiments, R1 is OH. In embodiments, Q is ribonucleic acid.

In embodiments, the R2-O—NH₂ molecule is independently one of:

In embodiments, the solution is an aqueous solution. In embodiments, thenucleotide is attached to a solid support and wherein the solid supportis in contact with the solution. In embodiments, the reagent thatincludes the structure R2-O—NH₂ is attached to a solid support incontact with the aqueous solution. In embodiments, the pH of thesolution is no less than 4 and no greater than 8.

In an aspect is provided a method of sequencing a nucleic acid includingthe steps:

-   -   A. making a 3′-blocked nucleotide using a method described        herein, including in embodiments, wherein the method of making        does not include isolating the 3′-blocked nucleotide from the        composition including the reactants and products of contacting        the 3′-protected nucleotide with the reagent;    -   B. contacting the composition including the 3′-blocked        nucleotide of step A with a nucleic acid template, primer, and        polymerase in a reaction vessel;    -   C. identifying the 3′-blocked nucleotide that simultaneously        contacts the template nucleic acid, 3′ terminus of the primer,        and polymerase; and optionally covalently binding the 3′-blocked        nucleotide to the 3′ terminus of the primer, making an extended        primer; and thereby identifying the cognate nucleotide of the        template nucleic acid to the 3′-blocking nucleotide;    -   D. removing the 3′-blocking moiety from the 3′-blocked        nucleotide of the extended primer of step C; and    -   E. repeating steps B to D and thereby sequencing the template        nucleic acid.

In embodiments, step E is executed at least 99 times. In embodiments,the composition includes reagent R2-ONH₂. In embodiments, the reagent R2is unsubstituted t-butyl. In embodiments, the reagent R2 is nothydrogen. In embodiments, the reagent R2 is not unsubstituted methyl. Inembodiments, the reagent R2 is not unsubstituted ethyl. In embodiments,the reagent R2 is not unsubstituted propyl. In embodiments, thecomposition does not include HONH₂. In embodiments, the composition doesnot include CH₃ONH₂.

In embodiments, the quality score of the sequencing is at least Q20. Inembodiments, the quality score of the sequencing is at least Q30. Inembodiments, the quality score of the sequencing is at least Q50.

In an aspect is provided a kit including a first vessel containing a3′-blocked nucleotide and a second vessel containing a reagent havingthe formula R2-O—NH₂, R2-O—NHCH₃, or R2-O—CH₂N₃ wherein R2 has amolecular weight of at least 24 g/mol.

In embodiments, the 3′-blocked nucleotide includes a blocking moietybonded directly to the ribose 3′ carbon of the nucleotide; and theblocking moiety is —ONH₂, —ONHCH₃, or —OCH₂CH₃. In embodiments, the3′-blocked nucleotide includes a blocking moiety bonded directly to theribose 3′ carbon of the nucleotide; and the blocking moiety is —ONH₂.

In embodiments, the 3′-protected nucleotide includes a protecting moietydirectly covalently bonded to the ribose 3′ carbon of the nucleotide;and the protecting moiety is a 3′ oxime moiety.

In embodiments, the —O-oxime moiety has the formula: —O—N═C(R3)(R4); andR3 and R4 are independently hydrogen, substituted or unsubstitutedalkyl, substituted or unsubstituted alkenyl, substituted orunsubstituted alkynyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedcycloalkenyl, substituted or unsubstituted cycloalkynyl, substituted orunsubstituted aryl, substituted or unsubstituted heteroaryl, substitutedor unsubstituted heteroalicyclyl, substituted or unsubstituted aralkyl,substituted or unsubstituted heteroaralkyl, or substituted orunsubstituted (heteroalicyclyl)alkyl.

In embodiments, the —O-oxime moiety has the formula: —O—N═C(R3)(R4); R3is hydrogen; and R4 is substituted or unsubstituted alkyl, substitutedor unsubstituted alkenyl, substituted or unsubstituted alkynyl,substituted or unsubstituted heteroalkyl, substituted or unsubstitutedcycloalkyl, substituted or unsubstituted cycloalkenyl, substituted orunsubstituted cycloalkynyl, substituted or unsubstituted aryl,substituted or unsubstituted heteroaryl, substituted or unsubstitutedheteroalicyclyl, substituted or unsubstituted aralkyl, substituted orunsubstituted heteroaralkyl, or substituted or unsubstituted(heteroalicyclyl)alkyl.

In embodiments, the —O-oxime moiety has the formula: —O—N═C(R3)(R4); andR3 and R4 are independently substituted or unsubstituted alkyl,substituted or unsubstituted alkenyl, substituted or unsubstitutedalkynyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl,substituted or unsubstituted cycloalkynyl, substituted or unsubstitutedaryl, substituted or unsubstituted heteroaryl, substituted orunsubstituted heteroalicyclyl, substituted or unsubstituted aralkyl,substituted or unsubstituted heteroaralkyl, or substituted orunsubstituted (heteroalicyclyl)alkyl.

In embodiments, the 3′-blocked nucleotide and the 3′-protectednucleotide include an adenine moiety or derivative thereof, guaninemoiety or derivative thereof, cytosine moiety or derivative thereof,thymine moiety or derivative thereof, or uracil moiety or derivativethereof. In embodiments, the adenine derivative moiety, guaninederivative moiety, cytosine derivative moiety, thymine derivativemoiety, and uracil derivative moiety include a detectable moiety. Inembodiments, the 3′-blocked nucleotide and the 3′-protected nucleotideinclude a monophosphate moiety or derivative thereof, diphosphate moietyor derivative thereof, triphosphate moiety or derivative thereof, ormonovalent nucleic acid moiety or derivative thereof. In embodiments,the 3′-blocked nucleotide and the 3′-protected nucleotide include amonophosphate moiety, diphosphate moiety, triphosphate moiety, ormonovalent nucleic acid moiety. In embodiments, the 3′-blockednucleotide and the 3′-protected nucleotide include a triphosphatemoiety. In embodiments, the 3′-blocked nucleotide and the 3′-protectednucleotide include a monovalent nucleic acid moiety. In embodiments, the3′-blocked nucleotide and the 3′-protected nucleotide include a ribosemoiety. In embodiments, the 3′-blocked nucleotide and the 3′-protectednucleotide include a 2′ deoxyribose moiety.

In embodiments, R2 has a molecular weight of 1000 g/mol or less. Inembodiments, R2 has a molecular weight of at least 36 g/mol. Inembodiments, R2 has a molecular weight of at least 57 g/mol.

In embodiments, R2 is substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl,substituted or unsubstituted cycloalkynyl, substituted or unsubstitutedaryl, substituted or unsubstituted heteroaryl, substituted orunsubstituted heteroalicyclyl, substituted or unsubstituted aralkyl,substituted or unsubstituted heteroaralkyl, or substituted orunsubstituted (heteroalicyclyl)alkyl. In embodiments, R2 is notunsubstituted methyl. In embodiments, R2 is not unsubstituted ethyl. Inembodiments, R2 is not unsubstituted propyl.

In embodiments, R2 is —C(R6)(R7)(R8), —C(O)(R6), —P(O)(R6)(R7),—C(R6)(═C(R7)(R8)), —Si(R6)(R7)(R8), —S O₂(R6), substituted orunsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl,substituted or unsubstituted cycloalkynyl, substituted or unsubstitutedheteroalicyclyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl; and R6, R7, and R8 are independently hydrogen,halogen, —CCl₃, —CBr₃, —CF₃, —CI₃, —CHCl₂, —CHBr₂, —CHF₂, —CHI₂, —CH₂Cl,—CH₂Br, —CH₂F, —CH₂I, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₃H,—SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂, —NHSO₂H,—NHC(O)H, —NHC(O)OH, —NHOH, —OCCl₃, —OCF₃, —OCBr₃, —OCI₃, —OCHCl₂,—OCHBr₂, —OCHI₂, —OCHF₂, —OCH₂Cl, —OCH₂Br, —OCH₂I, —OCH₂F, —SF₅, —N₃,substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted cycloalkenyl, substituted or unsubstitutedcycloalkynyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl, substituted or unsubstituted heteroalicyclyl,substituted or unsubstituted aralkyl, substituted or unsubstitutedheteroaralkyl, or substituted or unsubstituted (heteroalicyclyl)alkyl.In embodiments, R2 is —C(R6)(R7)(R8) and R6, R7, and R8 are not allhydrogen.

In embodiments, R2 is —C(R6)(R7)(R8), —C(O)(R6), —P(O)(R6)(R7),—C(R6)(═C(R7)(R8)), —Si(R6)(R7)(R8), —S O₂(R6), unsubstituted 6 memberedheteroalicyclyl, unsubstituted phenyl, substituted or unsubstitutedheteroaryl; and R6, R7, and R8 are independently hydrogen, halogen,—CCl₃, —CBr₃, —CF₃, —CI₃, —CHCl₂, —CHBr₂, —CHF₂, —CHI₂, —CH₂Cl, —CH₂Br,—CH₂F, —CH₂I, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₃H, —SO₄H,—SO₂NH₂, —NHNH₂, —ONH₂, —NIC(O)NHNH₂, —NHC(O)NH₂, —NHSO₂H, —NHC(O)H,—NHC(O)OH, —NHOH, —OCCl₃, —OCF₃, —OCBr₃, —OCI₃, —OCHCl₂, —OCHBr₂,—OCHI₂, —OCHF₂, —OCH₂Cl, —OCH₂Br, —OCH₂I, —OCH₂F, —SF₅, —N₃, substitutedor unsubstituted alkyl, substituted or unsubstituted alkenyl,substituted or unsubstituted alkynyl, substituted or unsubstitutedheteroalkyl, substituted or unsubstituted cycloalkyl, substituted orunsubstituted cycloalkenyl, substituted or unsubstituted cycloalkynyl,substituted or unsubstituted aryl, substituted or unsubstitutedheteroaryl, substituted or unsubstituted heteroalicyclyl, substituted orunsubstituted aralkyl, substituted or unsubstituted heteroaralkyl, orsubstituted or unsubstituted (heteroalicyclyl)alkyl. In embodiments, R2is —C(R6)(R7)(R8) and R6, R7, and R8 are not all hydrogen.

In embodiments, the reagent has the formula:

In embodiments, the reagent has the formula:

In embodiments, the 3′-protected nucleotide has the structure:

the 3′-blocked nucleotide has the structure:

B is a nucleobase; R1 is hydrogen, —OH, halogen, —OCH₃; Q isindependently a nucleic acid moiety, triphosphate moiety, diphosphatemoiety, or monophosphate moiety; and R3 and R4 are independentlyhydrogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl,substituted or unsubstituted cycloalkynyl, substituted or unsubstitutedaryl, substituted or unsubstituted heteroaryl, substituted orunsubstituted heteroalicyclyl, substituted or unsubstituted aralkyl,substituted or unsubstituted heteroaralkyl, or substituted orunsubstituted (heteroalicyclyl)alkyl.

In an aspect is provided a kit including a first vessel containing anucleotide including a 3′-O-oxime moiety and a second vessel containinga reagent including the structure R2-O—NH₂, wherein R2 is independentlyalkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl,heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl,(heteroalicyclyl)alkyl, or an optionally substituted variant thereof.

In embodiments, the nucleotide includes the structure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

In embodiments, the nucleobase is a purine or pyrimidine. Inembodiments, the nucleobase is independently adenine, cytosine, guanine,thymine, or uracil. In embodiments, the nucleobase is complementary toadenine, cytosine, guanine, thymine, or uracil. In embodiments, thenucleobase is independently 5-methylcytosine, hypoxanthine, xanthine,inosine, isoguanine, isocytosine, or 7-deazaguanine. In embodiments, thenucleobase includes an exogenous label moiety.

In embodiments, Q is independently a single stranded deoxyribonucleicacid or double stranded deoxyribonucleic acid.

In embodiments, the R2-O—NH₂ molecule is independently one of:

In embodiments, the kit includes an RFID tag or bar code.

In embodiments, the nucleotide is attached to a solid support. Inembodiments, the reagent that includes the structure R2-O—NH₂ isattached to a solid support.

In an aspect is provided a method of replacing a protecting group by ablocking group at a 3′ position of a nucleotide, including contactingthe nucleotide and a reagent including the structure R2-block, whereinR2 has a molecular weight of at least 24, wherein R2-block is watersoluble, and wherein block includes a blocking group moiety. Inembodiments, block comprises a reversible terminator moiety. Inembodiments, the reversible terminator moiety does not preclude assemblyof a nucleotide reversibly terminated thereby into a ternary complex.

In embodiments, R2-block is selected from the group consisting ofR2-O—NH₂, R2-O—NHCH₃, R2-O—NHCOCH₃, or R2-O—CH₂N₃. In embodiments,R2-block is R2-O—NH₂. In embodiments, R2-block is R2-O—NHCH₃. Inembodiments, R2-block is R2-O—NHCOCH₃. In embodiments, R2-block isR2-O—CH₂N₃.

In embodiments, the nucleotide including a 3′ protecting group is:

wherein the nucleotide including a 3′ blocking group is:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

In embodiments, the protecting group includes an O-oxime. Inembodiments, the oxime moiety has the formula: —O—N═C(R3)(R4); and R3and R4 are independently hydrogen, substituted or unsubstituted alkyl,substituted or unsubstituted alkenyl, substituted or unsubstitutedalkynyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl,substituted or unsubstituted cycloalkynyl, substituted or unsubstitutedaryl, substituted or unsubstituted heteroaryl, substituted orunsubstituted heteroalicyclyl, substituted or unsubstituted aralkyl,substituted or unsubstituted heteroaralkyl, or substituted orunsubstituted (heteroalicyclyl)alkyl. In embodiments, R3 is Hydrogen. Inembodiments, R4 is Hydrogen. In embodiments, the nucleotide comprises atriphosphate moiety.

In embodiments, R2 is —C(R6)(R7)(R8), —C(O)(R6), —P(O)(R6)(R7),—C(R6)(═C(R7)(R8)), —Si(R6)(R7)(R8), —S O₂(R6), substituted orunsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl,substituted or unsubstituted cycloalkynyl, substituted or unsubstitutedheteroalicyclyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl; and R6, R7, and R8 are independently hydrogen,halogen, —CCl₃, —CBr₃, —CF₃, —CI₃, —CHCl₂, —CHBr₂, —CHF₂, —CHI₂, —CH₂Cl,—CH₂Br, —CH₂F, —CH₂I, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₃H,—SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂, —NHSO₂H,—NHC(O)H, —NHC(O)OH, —NHOH, —OCCl₃, —OCF₃, —OCBr₃, —OCI₃, —OCHCl₂,—OCHBr₂, —OCHI₂, —OCHF₂, —OCH₂Cl, —OCH₂Br, —OCH₂I, —OCH₂F, —SF₅, —N₃,substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted cycloalkenyl, substituted or unsubstitutedcycloalkynyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl, substituted or unsubstituted heteroalicyclyl,substituted or unsubstituted aralkyl, substituted or unsubstitutedheteroaralkyl, or substituted or unsubstituted (heteroalicyclyl)alkyl.In embodiments, R2 is —C(R6)(R7)(R8) and R6, R7, and R8 are not allhydrogen.

In embodiments, R2-block has a formula selected from the groupconsisting of the following:

In embodiments, R2-block has a formula selected from the groupconsisting of:

In embodiments, R2-block has a formula

In embodiments, R2-block has a formula

In embodiments, R2-block has a formula

In embodiments, R2-block has a formula

In embodiments, R2-block has a formula

In embodiments, R2-block has a formula

In embodiments, R2-block has a formula

In embodiments, R2-block has a formula

In embodiments, R2-block has a formula

In embodiments, R2-block has a formula

In embodiments, R2-block has a formula

In embodiments, R2-block has a formula

In embodiments, R2-block has a formula

In embodiments, R2-block has a formula

In embodiments, R2-block has a formula

In embodiments, R2 comprises a hydroxylated moiety. In embodiments, R2comprises at least two carbon nuclei, a fluorine nucleus, carbon-carbondouble bond, tertiary carbon, tert-butyl moiety, cyclic moiety, siliconnucleus, phenyl ring, nitrogen nucleus, oxygen nucleus, or hydroxylatemoiety.

In embodiments, R2 has a molecular weight of no more than 280 g/mol. Inembodiments, R2 has a molecular weight of no more than 100 g/mol.

In embodiments, the method adds a blocking group in place of a 3′protecting group to at least 94% of a population of nucleotides having a3′ protecting group in no more than 3 hours at 25° C. In embodiments,the method adds a blocking group in place of a 3′ protecting group to atleast 98% of a population of nucleotides having a 3′ protecting group inno more than 3 hours at 25° C.

In embodiments, the method degrades no more than 6% of cytosinenucleobases in a population of nucleotides each comprising a cytosinenucleobase. In embodiments, the method degrades no more than 1% ofcytosine bases from the population of nucleotides having a cytosinenucleobase.

In embodiments, the composition includes (CH₃)₃C—ONH₂. In embodiments,the solution includes (CH₃)₃C—ONH₂. In embodiments, the aqueous solutionincludes (CH₃)₃C—ONH₂. In embodiments, the vessel includes (CH₃)₃C—ONH₂.In embodiments, the kit includes (CH₃)₃C—ONH₂. In embodiments, thecomposition does not include CH₃—ONH₂. In embodiments, the solution doesnot include CH₃—ONH₂. In embodiments, the aqueous solution does notinclude CH₃—ONH₂. In embodiments, the vessel does not include CH₃—ONH₂.In embodiments, the kit does not include CH₃—ONH₂. In embodiments, thecomposition does not include H—ONH₂. In embodiments, the solution doesnot include H—ONH₂. In embodiments, the aqueous solution does notinclude H—ONH₂. In embodiments, the vessel does not include H—ONH₂. Inembodiments, the kit does not include H—ONH₂.

Embodiments

Embodiment P1. A method for modifying a nucleotide, comprising reactinga nucleotide comprising a 3′-G-oxime moiety with a reagent comprisingthe structure R2-ONH₂ to produce a nucleotide comprising a 3′-G-NH₂moiety, wherein R2 is independently alkyl, alkenyl, alkynyl, cycloalkyl,cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl,heteroaralkyl, (heteroalicyclyl)alkyl, or an optionally substitutedvariant thereof.

Embodiment P2. The method of embodiment P1, wherein the nucleotide thatcomprises the 3′-O-oxime moiety comprises the structure:

wherein the nucleotide that comprises the 3′-O—NH₂ moiety comprises thestructure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

Embodiment P3. The method of embodiment P1, wherein the reaction occursin an aqueous solution.

Embodiment P4. The method of embodiment P3, wherein the nucleotide isattached to a solid support in contact with the aqueous solution.

Embodiment P5. The method of embodiment P3, wherein the reagent thatcomprises the structure R2-ONH₂ is attached to a solid support incontact with the aqueous solution.

Embodiment P6. The method of any one of embodiments P1 through P5,wherein the nucleobase is a purine or pyrimidine.

Embodiment P7. The method of embodiment P6, wherein the nucleobase isindependently adenine, cytosine, guanine, thymine, or uracil.

Embodiment P8. The method of embodiment P6, wherein the nucleobase iscomplementary to adenine, cytosine, guanine, thymine, or uracil.

Embodiment P9. The method of embodiment P6, wherein the nucleobase isindependently 5-methylcytosine, hypoxanthine, xanthine, inosine,isoguanine, isocytosine, or 7-deazaguanine.

Embodiment P10. The method of any one of embodiments P1 through P9,wherein the pH of the solution is between 4 and 8.

Embodiment P11. The method of any one of embodiments P1 through P10,wherein the nucleotide that is produced comprises a deoxynucleotide.

Embodiment P12. The method of embodiment P11, wherein the nucleotidethat is produced comprises:

wherein Base is the nucleobase, and wherein DNA is independently asingle stranded deoxyribonucleic acid or double strandeddeoxyribonucleic acid.

Embodiment P13. The method of any one of embodiments P1 through P12,wherein the reagent is independently one of:

Embodiment P14. A solution comprising a nucleotide comprising a3′-O-oxime moiety and a reagent comprising the structure R2-ONH₂,wherein R2 is independently alkyl, alkenyl, alkynyl, cycloalkyl,cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl,heteroaralkyl, (heteroalicyclyl)alkyl, or an optionally substitutedvariant thereof.

Embodiment P15. The solution of embodiment P14, wherein the nucleotidecomprises the structure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

Embodiment P16. The solution of embodiment P15, wherein R1 is H.

Embodiment P17. The solution of embodiment P16, wherein Q isdeoxyribonucleic acid.

Embodiment P18. The solution of embodiment P15, wherein R1 is OH.

Embodiment P19. The solution of embodiment P18, wherein Q is ribonucleicacid.

Embodiment P20. The solution of embodiment P14, wherein the solution isan aqueous solution.

Embodiment P21. The solution of embodiment P20, wherein the nucleotideis attached to a solid support and wherein the solid support is incontact with the solution.

Embodiment P22. The solution of embodiment P20, wherein the reagent thatcomprises the structure R2-ONH₂ is attached to a solid support incontact with the aqueous solution.

Embodiment P23. The solution of any one of embodiments P14 through P2A3,wherein the nucleobase is a purine or pyrimidine.

Embodiment P24. The solution of embodiment P23, wherein the nucleobaseis independently adenine, cytosine, guanine, thymine, or uracil.

Embodiment P25. The solution of embodiment P23, wherein the nucleobaseis complementary to adenine, cytosine, guanine, thymine, or uracil.

Embodiment P26. The solution of embodiment P23, wherein the nucleobaseis independently 5-methylcytosine, hypoxanthine, xanthine, inosine,isoguanine, isocytosine, or 7-deazaguanine.

Embodiment P27. The solution of any one of embodiments P14 through P26,wherein the nucleobase comprises an exogenous label moiety.

Embodiment P28. The solution of any one of embodiments P14 through P27,wherein the pH of the solution is between 4 and 8.

Embodiment P29. The solution of any one of embodiments P14 through P28,wherein the R2-ONH₂ molecule is independently one of:

Embodiment P30. A kit comprising a first vessel containing a nucleotidecomprising a 3′-O-oxime moiety and a second vessel containing a reagentcomprising the structure R2-ONH₂, wherein R2 is independently alkyl,alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl,heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl,(heteroalicyclyl)alkyl, or an optionally substituted variant thereof.

Embodiment P31. The kit of embodiment P30, wherein the nucleotidecomprises the structure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

Embodiment P32. The kit of embodiment P30, wherein the kit comprises anRFID tag or bar code.

Embodiment P33. The kit of embodiment P31 or P32, wherein Q isindependently a single stranded deoxyribonucleic acid or double strandeddeoxyribonucleic acid.

Embodiment P34. The kit of embodiment P33, wherein the nucleotide isattached to a solid support.

Embodiment P35. The kit of embodiment P30, wherein the reagent thatcomprises the structure R2-ONH₂ is attached to a solid support.

Embodiment P36. The kit of any one of embodiments P30 through P35,wherein the nucleobase is a purine or pyrimidine.

Embodiment P38. The kit of embodiment P36, wherein the nucleobase isindependently adenine, cytosine, guanine, thymine, or uracil.

Embodiment P39. The kit of embodiment P36, wherein the nucleobase iscomplementary to adenine, cytosine, guanine, thymine, or uracil.

Embodiment P40. The kit of embodiment P36, wherein the nucleobase isindependently 5-methylcytosine, hypoxanthine, xanthine, inosine,isoguanine, isocytosine, or 7-deazaguanine.

Embodiment P41. The kit of any one of embodiments P30 through P40,wherein the nucleobase comprises an exogenous label moiety.

Embodiment P42. The kit of any one of embodiments P30 through P41,wherein the R2-ONH₂ molecule is independently one of:

Embodiment PP1. A method for modifying a nucleotide, comprising reactinga nucleotide comprising a 3′-O-oxime moiety with a reagent comprisingthe structure R2-ONH₂ to produce a nucleotide comprising a 3′-O—NH₂moiety, wherein R2 is independently alkyl, alkenyl, alkynyl, cycloalkyl,cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl,heteroaralkyl, (heteroalicyclyl)alkyl, or an optionally substitutedvariant thereof.

Embodiment PP2. The method of embodiment PP1, wherein the nucleotidethat comprises the 3′-O-oxime moiety comprises the structure:

wherein the nucleotide that comprises the 3′-O—NH₂ moiety comprises thestructure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

Embodiment PP3. The method of embodiment PP1, wherein the reactionoccurs in an aqueous solution.

Embodiment PP4. The method of embodiment PP3, wherein the nucleotide isattached to a solid support in contact with the aqueous solution.

Embodiment PP5. The method of embodiment PP3, wherein the reagent thatcomprises the structure R2-ONH₂ is attached to a solid support incontact with the aqueous solution.

Embodiment PP6. The method of any one of embodiments PP1 through PP5,wherein the nucleobase is a purine or pyrimidine.

Embodiment PP7. The method of embodiment PP6, wherein the nucleobase isindependently adenine, cytosine, guanine, thymine, or uracil.

Embodiment PP8. The method of embodiment PP6, wherein the nucleobase iscomplementary to adenine, cytosine, guanine, thymine, or uracil.

Embodiment PP9. The method of embodiment PP6, wherein the nucleobase isindependently 5-methylcytosine, hypoxanthine, xanthine, inosine,isoguanine, isocytosine, or 7-deazaguanine.

Embodiment PP10. The method of any one of embodiments PP1 through PP9,wherein the pH of the solution is between 4 and 8.

Embodiment PP11. The method of any one of embodiments PP1 through PP10,wherein the nucleotide that is produced comprises a deoxynucleotide.

Embodiment PP12. The method of embodiment PP11, wherein the nucleotidethat is produced comprises:

wherein Base is the nucleobase, and wherein DNA is independently asingle stranded deoxyribonucleic acid or double strandeddeoxyribonucleic acid.

Embodiment PP13. The method of any one of embodiments PP1 through PP12,wherein the reagent is independently one of:

Embodiment PP14. A solution comprising a nucleotide comprising a3′-O-oxime moiety and a reagent comprising the structure R2-ONH₂,wherein R2 is independently alkyl, alkenyl, alkynyl, cycloalkyl,cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl,heteroaralkyl, (heteroalicyclyl)alkyl, or an optionally substitutedvariant thereof.

Embodiment PP15. The solution of embodiment PP14, wherein the nucleotidecomprises the structure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

Embodiment PP16. The solution of embodiment PP15, wherein R1 is H.

Embodiment PP17. The solution of embodiment PP16, wherein Q isdeoxyribonucleic acid.

Embodiment PP18. The solution of embodiment PP15, wherein R1 is OH.

Embodiment PP19. The solution of embodiment PP18, wherein Q isribonucleic acid.

Embodiment PP20. The solution of embodiment PP14, wherein the solutionis an aqueous solution.

Embodiment PP21. The solution of embodiment PP20, wherein the nucleotideis attached to a solid support and wherein the solid support is incontact with the solution.

Embodiment PP22. The solution of embodiment PP20, wherein the reagentthat comprises the structure R2-ONH₂ is attached to a solid support incontact with the aqueous solution.

Embodiment PP23. The solution of any one of embodiments PP14 throughPP22, wherein the nucleobase is a purine or pyrimidine.

Embodiment PP24. The solution of embodiment PP23, wherein the nucleobaseis independently adenine, cytosine, guanine, thymine, or uracil.

Embodiment PP25. The solution of embodiment PP23, wherein the nucleobaseis complementary to adenine, cytosine, guanine, thymine, or uracil.

Embodiment PP26. The solution of embodiment PP23, wherein the nucleobaseis independently 5-methylcytosine, hypoxanthine, xanthine, inosine,isoguanine, isocytosine, or 7-deazaguanine.

Embodiment PP27. The solution of any one of embodiments PP14 throughPP26, wherein the nucleobase comprises an exogenous label moiety.

Embodiment PP28. The solution of any one of embodiments PP14 throughPP27, wherein the pH of the solution is between 4 and 8.

Embodiment PP29. The solution of any one of embodiments PP14 throughPP28, wherein the R2-ONH₂ molecule is independently one of:

Embodiment PP30. A kit comprising a first vessel containing a nucleotidecomprising a 3′-O-oxime moiety and a second vessel containing a reagentcomprising the structure R2-ONH₂, wherein R2 is independently alkyl,alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl,heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl,(heteroalicyclyl)alkyl, or an optionally substituted variant thereof.

Embodiment PP31. The kit of embodiment PP30, wherein the nucleotidecomprises the structure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

Embodiment PP32. The kit of embodiment PP30, wherein the kit comprisesan RFID tag or bar code.

Embodiment PP33. The kit of embodiment PP31 or PP32, wherein Q isindependently a single stranded deoxyribonucleic acid or double strandeddeoxyribonucleic acid.

Embodiment PP34. The kit of embodiment PP33, wherein the nucleotide isattached to a solid support.

Embodiment PP35. The kit of embodiment PP30, wherein the reagent thatcomprises the structure R2-ONH₂ is attached to a solid support.

Embodiment PP36. The kit of any one of embodiments PP30 through PP35,wherein the nucleobase is a purine or pyrimidine.

Embodiment PP38. The kit of embodiment PP36, wherein the nucleobase isindependently adenine, cytosine, guanine, thymine, or uracil.

Embodiment PP39. The kit of embodiment PP36, wherein the nucleobase iscomplementary to adenine, cytosine, guanine, thymine, or uracil.

Embodiment PP40. The kit of embodiment PP36, wherein the nucleobase isindependently 5-methylcytosine, hypoxanthine, xanthine, inosine,isoguanine, isocytosine, or 7-deazaguanine.

Embodiment PP41. The kit of any one of embodiments PP30 through PP40,wherein the nucleobase comprises an exogenous label moiety.

Embodiment PP42. The kit of any one of embodiments PP30 through PP41,wherein the R2-ONH₂ molecule is independently one of:

Further Embodiments

Embodiment Si. A method of adding a 3′-O—NH₂ moiety to a nucleotidehaving a 3′ protecting group, comprising contacting a nucleotide havinga 3′ protecting group to a reagent comprising the structure R2-O—NH₂,wherein R2 has a molecular weight of at least 24.

Embodiment S2. The method of embodiment S1, wherein the nucleotidehaving a 3′ protecting group comprises ribose or deoxyribose.

Embodiment S3. The method of embodiment S2, wherein the nucleotidehaving a 3′ protecting group comprises triphosphate.

Embodiment S4. The method of embodiment S1, wherein the nucleotidehaving a 3′ protecting group comprises the structure:

wherein the nucleotide that comprises the 3′-O—NH₂ moiety comprises thestructure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

Embodiment S5. A method of making a 3′-blocked nucleotide, the methodcomprising contacting a 3′-protected nucleotide with a reagent havingthe structure R2-O—NH₂, R2-O—NHCH₃, R2-O—NHCOCH₃, or R2-O—CH₂N₃ whereinR2 has a molecular weight of at least 24 g/mol and thereby making a3′-blocked nucleotide from a 3′-protected nucleotide.

Embodiment S6. A method of making a 3′-blocked nucleotide, the methodcomprising contacting a 3′-protected nucleotide with a reagent havingthe structure R2-O—NH₂ or R2-O—CH₂N₃ wherein R2 has a molecular weightof at least 24 g/mol and thereby making a 3′-blocked nucleotide from a3′-protected nucleotide.

Embodiment S7. The method of embodiment S5, wherein the 3′-blockednucleotide comprises a blocking moiety bonded directly to the ribose 3′carbon of the nucleotide; and the blocking moiety is —ONH₂, —ONHCOCH₃,—ONHCH₃, —OCH₂N₃.

Embodiment S8. The method of one of embodiments S5 to S6, wherein the3′-blocked nucleotide comprises a blocking moiety bonded directly to theribose 3′ carbon of the nucleotide; and the blocking moiety is —ONH₂ or—OCH₂N₃.

Embodiment S9. The method of one of embodiments S5 to S6, wherein the3′-blocked nucleotide comprises a blocking moiety bonded directly to theribose 3′ carbon of the nucleotide; and the blocking moiety is —ONH₂.

Embodiment S10. The method of one of embodiments S5 to S9, wherein the3′-protected nucleotide comprises a protecting moiety directlycovalently bonded to the ribose 3′ carbon of the nucleotide; and theprotecting moiety is a 3′-O-oxime moiety.

Embodiment S11. The method of embodiment S10, wherein the —O-oximemoiety has the formula:

—O—N═C(R3)(R4); and

R3 and R4 are independently hydrogen, substituted or unsubstitutedalkyl, substituted or unsubstituted alkenyl, substituted orunsubstituted alkynyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedcycloalkenyl, substituted or unsubstituted cycloalkynyl, substituted orunsubstituted aryl, substituted or unsubstituted heteroaryl, substitutedor unsubstituted heteroalicyclyl, substituted or unsubstituted aralkyl,substituted or unsubstituted heteroaralkyl, or substituted orunsubstituted (heteroalicyclyl)alkyl.

Embodiment S12. The method of embodiment S10, wherein the —O-oximemoiety has the formula:

—O—N═C(R3)(R4);

R3 is hydrogen; andR4 is substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted cycloalkenyl, substituted or unsubstitutedcycloalkynyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl, substituted or unsubstituted heteroalicyclyl,substituted or unsubstituted aralkyl, substituted or unsubstitutedheteroaralkyl, or substituted or unsubstituted (heteroalicyclyl)alkyl.

Embodiment S13. The method of embodiment S10, wherein the —O-oximemoiety has the formula:

—O—N═C(R3)(R4); and

R3 and R4 are independently substituted or unsubstituted alkyl,substituted or unsubstituted alkenyl, substituted or unsubstitutedalkynyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl,substituted or unsubstituted cycloalkynyl, substituted or unsubstitutedaryl, substituted or unsubstituted heteroaryl, substituted orunsubstituted heteroalicyclyl, substituted or unsubstituted aralkyl,substituted or unsubstituted heteroaralkyl, or substituted orunsubstituted (heteroalicyclyl)alkyl.

Embodiment S14. The method of one of embodiments S5 to S13, wherein the3′-blocked nucleotide and the 3′-protected nucleotide comprise anadenine moiety or derivative thereof, guanine moiety or derivativethereof, cytosine moiety or derivative thereof, thymine moiety orderivative thereof, or uracil moiety or derivative thereof.

Embodiment S15. The method of embodiment S14, wherein the adeninederivative moiety, guanine derivative moiety, cytosine derivativemoiety, thymine derivative moiety, and uracil derivative moiety comprisea detectable moiety.

Embodiment S16. The method of one of embodiments S5 to S15, wherein the3′-blocked nucleotide and the 3′-protected nucleotide comprise amonophosphate moiety or derivative thereof, diphosphate moiety orderivative thereof, triphosphate moiety or derivative thereof, ormonovalent nucleic acid moiety or derivative thereof.

Embodiment S17. The method of embodiment S16, wherein the 3′-blockednucleotide and the 3′-protected nucleotide comprise a monophosphatemoiety, diphosphate moiety, triphosphate moiety, or monovalent nucleicacid moiety.

Embodiment S18. The method of embodiment S16, wherein the 3′-blockednucleotide and the 3′-protected nucleotide comprise a triphosphatemoiety.

Embodiment S19. The method of embodiment S16, wherein the 3′-blockednucleotide and the 3′-protected nucleotide comprise a monovalent nucleicacid moiety.

Embodiment S20. The method of one of embodiments S5 to S19, wherein the3′-blocked nucleotide and the 3′-protected nucleotide comprise a ribosemoiety.

Embodiment S21. The method of one of embodiments S5 to S19, wherein the3′-blocked nucleotide and the 3′-protected nucleotide comprise a 2′deoxyribose moiety.

Embodiment S22. The method of one of embodiments S1 to S21, wherein R2has a molecular weight of 1000 g/mol or less.

Embodiment S23. The method of one of embodiments S1 to S22, wherein R2has a molecular weight of at least 36 g/mol.

Embodiment S24. The method of one of embodiments S1 to S22, wherein R2has a molecular weight of at least 57 g/mol.

Embodiment S25. The method of one of embodiments S1 to S22, wherein R2comprises at least two carbon nuclei, a fluorine nucleus, carbon-carbondouble bond, tertiary carbon, tert-butyl moiety, cyclic moiety, siliconnucleus, phenyl ring, nitrogen nucleus, oxygen nucleus, or hydroxylatemoiety.

Embodiment S26. The method of one of embodiments S1 to S22, wherein R2is substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted cycloalkenyl, substituted or unsubstitutedcycloalkynyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl, substituted or unsubstituted heteroalicyclyl,substituted or unsubstituted aralkyl, substituted or unsubstitutedheteroaralkyl, or substituted or unsubstituted (heteroalicyclyl)alkyl.

Embodiment S27. The method of one of embodiments S1 to S22, wherein R2is —C(R6)(R7)(R8), —C(O)(R6), —P(O)(R6)(R7), —C(R6)(═C(R7)(R8)),—Si(R6)(R7)(R8), —S O₂(R6), substituted or unsubstituted cycloalkyl,substituted or unsubstituted cycloalkenyl, substituted or unsubstitutedcycloalkynyl, substituted or unsubstituted heteroalicyclyl, substitutedor unsubstituted aryl, substituted or unsubstituted heteroaryl; and

R6, R7, and R8 are independently hydrogen,halogen, —CCl₃, —CBr₃, —CF₃, —CI₃, —CHCl₂, —CHBr₂, —CHF₂, —CHI₂, —CH₂Cl,—CH₂Br, —CH₂F, —CH₂I, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₃H,—SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂, —NHSO₂H,—NHC(O)H, —NHC(O)OH, —NHOH, —OCCl₃, —OCF₃, —OCBr₃, —OCI₃, —OCHCl₂,—OCHBr₂, —OCHI₂, —OCHF₂, —OCH₂Cl, —OCH₂Br, —OCH₂I, —OCH₂F, —SF₅, —N₃,substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted cycloalkenyl, substituted or unsubstitutedcycloalkynyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl, substituted or unsubstituted heteroalicyclyl,substituted or unsubstituted aralkyl, substituted or unsubstitutedheteroaralkyl, or substituted or unsubstituted (heteroalicyclyl)alkyl.

Embodiment S28. The method of embodiment S27, wherein R2 is—C(R6)(R7)(R8) and R6, R7, and R8 are not all hydrogen.

Embodiment S29. The method of embodiment S27, wherein R2 is notunsubstituted methyl.

Embodiment S30. The method of embodiment S27, wherein R2 is notunsubstituted ethyl.

Embodiment S31. The method of embodiment S27, wherein R2 is notunsubstituted propyl.

Embodiment 532. The method of one of embodiments S1 to S22, wherein R2is —C(R6)(R7)(R8), —C(O)(R6), —P(O)(R6)(R7), —C(R6)(═C(R7)(R8)),—Si(R6)(R7)(R8), —S O₂(R6), unsubstituted 6 membered heteroalicyclyl,unsubstituted phenyl, substituted or unsubstituted heteroaryl; and

R6, R7, and R8 are independently hydrogen,halogen, —CCl₃, —CBr₃, —CF₃, —CI₃, —CHCl₂, —CHBr₂, —CHF₂, —CHI₂, —CH₂Cl,—CH₂Br, —CH₂F, —CH₂I, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₃H,—SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂, —NHSO₂H,—NHC(O)H, —NHC(O)OH, —NHOH, —OCCl₃, —OCF₃, —OCBr₃, —OCI₃, —OCHCl₂,—OCHBr₂, —OCHI₂, —OCHF₂, —OCH₂Cl, —OCH₂Br, —OCH₂I, —OCH₂F, —SF₅, —N₃,substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted cycloalkenyl, substituted or unsubstitutedcycloalkynyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl, substituted or unsubstituted heteroalicyclyl,substituted or unsubstituted aralkyl, substituted or unsubstitutedheteroaralkyl, or substituted or unsubstituted (heteroalicyclyl)alkyl.

Embodiment S33. The method of embodiment S32, wherein R2 is—C(R6)(R7)(R8) and R6, R7, and R8 are not all hydrogen.

Embodiment S34. The method of embodiment S32, wherein R2 is notunsubstituted methyl.

Embodiment S35. The method of embodiment S32, wherein R2 is notunsubstituted ethyl.

Embodiment S36. The method of embodiment S32, wherein R2 is notunsubstituted propyl.

Embodiment S37. The method of one of embodiments S1 to S22, wherein thereagent has the formula:

Embodiment S38. The method of one of embodiments S1 to S22, wherein thereagent has the formula:

Embodiment S39. The method of one of embodiments S5 to S11, wherein the3′-protected nucleotide has the structure:

the 3′-blocked nucleotide has the structure:

B is a nucleobase;R1 is hydrogen, —OH, halogen, —OCH₃;Q is independently a nucleic acid moiety, triphosphate moiety,diphosphate moiety, or monophosphate moiety;R3 and R4 are independently hydrogen, substituted or unsubstitutedalkyl, substituted or unsubstituted alkenyl, substituted orunsubstituted alkynyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedcycloalkenyl, substituted or unsubstituted cycloalkynyl, substituted orunsubstituted aryl, substituted or unsubstituted heteroaryl, substitutedor unsubstituted heteroalicyclyl, substituted or unsubstituted aralkyl,substituted or unsubstituted heteroaralkyl, or substituted orunsubstituted (heteroalicyclyl)alkyl.

Embodiment S40. The method of one of embodiments S1 to S4, wherein themethod adds a 3′ ONH₂ in place of a 3′ protecting group to at least 94%of a population of nucleotides having a 3′ protecting group in no morethan 3 hours.

Embodiment S41. The method of one of embodiments S1 to S4, wherein themethod adds a 3′ ONH₂ in place of a 3′ protecting group to at least 98%of a population of nucleotides having a 3′ protecting group in no morethan 1 hour.

Embodiment S42. The method of one of embodiments S1 to S4, wherein thenucleotide having a 3′ protecting group comprises cytosine, and whereinmethod degrades no more than 6% of cytosine bases from a populationcomprising a plurality of said nucleotide having a 3′ protecting groupcomprising cytosine.

Embodiment S43. The method of one of embodiments S1 to S4, wherein thenucleotide having a 3′ protecting group comprises cytosine, and whereinmethod degrades no more than 1% of cytosine bases from a populationcomprising a plurality of said nucleotide having a 3′ protecting groupcomprising cytosine.

Embodiment S44. The method of one of embodiments S5 to S39, furthercomprising making a first plurality of 3′-blocked nucleotides, themethod comprising contacting a second plurality of 3′-protectednucleotides with a third plurality of the reagent and thereby making afirst plurality of 3′-blocked nucleotides from a second plurality of3′-protected nucleotides.

Embodiment S45. The method of embodiment S44, wherein the firstplurality of 3′-blocked nucleotides are made for 3 hours or less.

Embodiment S46. The method of embodiment S44, wherein the firstplurality of 3′-blocked nucleotides are made for 2 hours or less.

Embodiment S47. The method of embodiment S44, wherein the firstplurality of 3′-blocked nucleotides are made for 1 hour or less.

Embodiment S48. The method of one of embodiments S44 to S47, wherein atleast 94% of the first plurality of 3′-protected nucleotide is made intothe second plurality of 3′-blocked nucleotides.

Embodiment S49. The method of one of embodiments S44 to S47, wherein atleast 96% of the first plurality of 3′-protected nucleotide is made intothe second plurality of 3′-blocked nucleotides.

Embodiment S50. The method of one of embodiments S44 to S47, wherein atleast 98% of the first plurality of 3′-protected nucleotide is made intothe second plurality of 3′-blocked nucleotides.

Embodiment S51. The method of one of embodiments S44 to S50, wherein thefirst plurality of 3′-blocked nucleotides comprises a fourth pluralityof 3′-blocked nucleotides comprising a cytosine; and 6% or less of thecytosines are chemically modified by the third plurality of the reagent.

Embodiment S52. The method of one of embodiments S44 to S50, wherein thefirst plurality of 3′-blocked nucleotides comprises a fourth pluralityof 3′-blocked nucleotides comprising a cytosine; and 5% or less of thecytosines are chemically modified by the third plurality of the reagent.

Embodiment S53. The method of one of embodiments S44 to S50, wherein thefirst plurality of 3′-blocked nucleotides comprises a fourth pluralityof 3′-blocked nucleotides comprising a cytosine; and 4% or less of thecytosines are chemically modified by the third plurality of the reagent.

Embodiment S54. The method of one of embodiments S44 to S50, wherein thefirst plurality of 3′-blocked nucleotides comprises a fourth pluralityof 3′-blocked nucleotides comprising a cytosine; and 3% or less of thecytosines are chemically modified by the third plurality of the reagent.

Embodiment S55. The method of one of embodiments S44 to S50, wherein thefirst plurality of 3′-blocked nucleotides comprises a fourth pluralityof 3′-blocked nucleotides comprising a cytosine; and 2% or less of thecytosines are chemically modified by the third plurality of the reagent.

Embodiment S56. The method of one of embodiments S44 to S50, wherein thefirst plurality of 3′-blocked nucleotides comprises a fourth pluralityof 3′-blocked nucleotides comprising a cytosine; and 1% or less of thecytosines are chemically modified by the third plurality of the reagent.

Embodiment S57. A composition comprising a population of cytosinenucleotides wherein at least 94% of the population of cytosinenucleotides comprise a 3′-O—NH₂, wherein no more than 8% of thepopulation of cytosine nucleotides comprise a 3′ moiety other than—O—NH₂, and wherein no more than 6% of the population of cytosinenucleotides comprise a modified cytosine base.

Embodiment S58. The composition of embodiment S57, wherein at least 98%of the population of cytosine nucleotides comprise a 3′-O—NH₂, whereinno more than 1% of the population of cytosine nucleotides comprise a 3′moiety other than —O—NH₂, and wherein no more than 1% of the populationof cytosine nucleotides comprise a modified cytosine base.

Embodiment S59. The composition of embodiment S57, wherein thecomposition is an aqueous solution.

Embodiment S60. The composition of embodiment S57, wherein the pH of thesolution is no less than 4 and no greater than 8.

Embodiment S61. The composition of embodiment S57, wherein thecomposition comprises a reagent comprising the structure R2-O—NH₂.

Embodiment S62. The composition of embodiment S61, wherein R2 comprisesa molecular weight of at least 24, 26, 57, or 100.

Embodiment S63. The composition of embodiment S61, wherein R2 comprisesat least two carbon nuclei, a fluorine nucleus, carbon-carbon doublebond, tertiary carbon, tert-butyl moiety, cyclic moiety, siliconnucleus, phenyl ring, nitrogen nucleus, oxygen nucleus, or hydroxylatemoiety.

Embodiment S64. The composition of embodiment S61, wherein the reagentcomprising the structure R2-O—NH₂ is selected from the group consistingof:

Embodiment S65. The composition of one of embodiments S57 to S64,wherein the 3′ moiety other than —O—NH₂ comprises a 3′ O-oxime.

Embodiment S66. The composition of embodiment S57, wherein thecomposition comprises a reagent comprising the structure R2-O—NHCH₃ orR2-O—CH₂N₃.

Embodiment S67. The composition of one of embodiments S57 to S66,wherein at least some of the cytosine nucleotides having a 3′ moietyother than —O—NH₂ nucleotide comprise the structure:

wherein B is a cytosine nucleobase; R1 is independently halogen, OCH₃, Hor OH, Q is independently monophosphate, diphosphate, triphosphate, ornucleic acid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl,alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

Embodiment S68. A method of formulating a sequencing reagent, comprisingcontacting a composition comprising a 3′ protected nucleotide to areagent comprising a reversible terminator moiety to produce acomposition comprising a nucleotide comprising a reversible terminatormoiety, and formulating the composition comprising a nucleotidecomprising a reversible terminator moiety as a sequencing reagent,wherein formulating the composition comprising a reversible terminatormoiety does not comprise further purification of the compositioncomprising a reversible terminator moiety.

Embodiment S69. The method of embodiment S68, further comprisingapplying the sequencing reagent to a sequencing reagent to yield asequencing run of at least 100 bases having a quality score of at leastQ30.

Embodiment S70. The method of embodiment S68, wherein the reagentcomprising a reversible terminator moiety has a structure R2-O—NH₂.

Embodiment S71. The method of embodiment S70, wherein R2 is selectedfrom the group consisting of —C(R6)(R7)(R8), —C(O)(R6), —P(O)(R6)(R7),—C(R6)(═C(R7)(R8)), —Si(R6)(R7)(R8), —S O₂(R6), substituted orunsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl,substituted or unsubstituted cycloalkynyl, substituted or unsubstitutedheteroalicyclyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl; and R6, R7, and R8 are independently hydrogen,halogen, —CCl₃, —CBr₃, —CF₃, —CI₃, —CHCl₂, —CHBr₂, —CHF₂, —CHI₂, —CH₂Cl,—CH₂Br, —CH₂F, —CH₂I, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₃H,—SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC(O)NHINH₂, —NHC(O)NH₂, —NHSO₂H,—NHC(O)H, —NHC(O)OH, —NHOH, —OCCl₃, —OCF₃, —OCBr₃, —OCI₃, —OCHCl₂,—OCHBr₂, —OCHI₂, —OCHF₂, —OCH₂Cl, —OCH₂Br, —OCH₂I, —OCH₂F, —SF₅, —N₃,substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted cycloalkenyl, substituted or unsubstitutedcycloalkynyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl, substituted or unsubstituted heteroalicyclyl,substituted or unsubstituted aralkyl, substituted or unsubstitutedheteroaralkyl, or substituted or unsubstituted (heteroalicyclyl)alkyl.

Embodiment S72. The method of embodiment S71, wherein R2 is—C(R6)(R7)(R8) and R6, R7, and R8 are not all hydrogen.

Embodiment S73. The method of embodiment S71, wherein R2 is notunsubstituted methyl.

Embodiment S74. The method of embodiment S71, wherein R2 is notunsubstituted ethyl.

Embodiment S75. The method of embodiment S71, wherein R2 is notunsubstituted propyl.

Embodiment S76. The method of embodiment S70, wherein R2 is —C(CH₃)₃.

Embodiment S77. The method of embodiment S70, wherein R2 has a molecularweight greater than 24, 36, 57, or 100.

Embodiment S78. The method of embodiment S70, wherein R2 comprises atleast two carbon nuclei, a fluorine nucleus, carbon-carbon double bond,tertiary carbon, tert-butyl moiety, cyclic moiety, silicon nucleus,phenyl ring, nitrogen nucleus, oxygen nucleus, or hydroxylate moiety.

Embodiment S79. The method of embodiment S68, wherein the 3′ protectednucleotide comprises a 3′-O-oxime moiety.

Embodiment S80. The method of embodiment S68, wherein the compositioncomprising a nucleotide comprising a reversible terminator moietycomprises no more than 6% of the 3′ protected nucleotide relative to 3′protected nucleotide present initially.

Embodiment S81. The method of embodiment S68, wherein the compositioncomprising a nucleotide comprising a reversible terminator moietycomprises degraded or modified dC nucleobases at a concentration of nomore than 6% of total dC nucleobases in the composition comprising anucleotide comprising a reversible terminator moiety.

Embodiment S82. A method for modifying a nucleotide, comprising reactinga nucleotide comprising a 3′-O-oxime moiety with a reagent comprisingthe structure R2-O—NH₂ to produce a nucleotide comprising a 3′-O—NH₂moiety, wherein R2 is independently alkyl, alkenyl, alkynyl, cycloalkyl,cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl,heteroaralkyl, (heteroalicyclyl)alkyl, or an optionally substitutedvariant thereof.

Embodiment S83. The method of embodiment S82, wherein the nucleotidethat comprises the 3′-O-oxime moiety comprises the structure:

wherein the nucleotide that comprises the 3′-O—NH₂ moiety comprises thestructure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

Embodiment S84. The method of one of embodiments S82 to S83, wherein thenucleotide that is produced comprises a deoxynucleotide.

Embodiment S85. The method of embodiment S82, wherein the nucleotidethat is produced comprises:

wherein Base is the nucleobase, and wherein DNA is independently asingle stranded deoxyribonucleic acid or double strandeddeoxyribonucleic acid.

Embodiment S86. The method of any one of embodiments S82 to S85, whereinthe reagent is independently one of:

Embodiment S87. A solution comprising a nucleotide comprising a3′-O-oxime moiety and a reagent comprising the structure R2-O—NH₂,wherein R2 is independently alkyl, alkenyl, alkynyl, cycloalkyl,cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl,heteroaralkyl, (heteroalicyclyl)alkyl, or an optionally substitutedvariant thereof.

Embodiment S88. The solution of embodiment S87, wherein the nucleotidecomprises the structure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

Embodiment S89. The solution of one of embodiments S87 to S88, whereinthe nucleobase comprises an exogenous label moiety.

Embodiment S90. The solution of one of embodiments S87 to S89, whereinthe R2-O—NH₂ molecule is independently one of:

Embodiment S91. A method of sequencing a nucleic acid comprising thesteps:

-   -   A. making a 3′-blocked nucleotide using the method of one of        embodiments S5 to S56, wherein the method of making does not        comprise isolating the 3′-blocked nucleotide from the        composition comprising the reactants and products of contacting        the 3′-protected nucleotide with the reagent;    -   B. contacting the composition comprising the 3′-blocked        nucleotide of step A with a nucleic acid template, primer, and        polymerase in a reaction vessel;    -   C. identifying the 3′-blocked nucleotide that simultaneously        contacts the template nucleic acid, 3′ terminus of the primer,        and polymerase; and optionally covalently binding the 3′-blocked        nucleotide to the 3′ terminus of the primer, making an extended        primer; and thereby identifying the cognate nucleotide of the        template nucleic acid to the 3′-blocking nucleotide;    -   D. removing the 3′-blocking moiety from the 3′-blocked        nucleotide of the extended primer of step C; and    -   E. repeating steps B to D and thereby sequencing the template        nucleic acid.

Embodiment S92. The method of embodiment S91, wherein step E is executedat least 99 times.

Embodiment S93. The method of one of embodiments S91 to S92, wherein thequality score of the sequencing is at least Q20.

Embodiment S94. The method of one of embodiments S91 to S92, wherein thequality score of the sequencing is at least Q30.

Embodiment S95 The method of one of embodiments S91 to S92, wherein thequality score of the sequencing is at least Q50.

Embodiment S96. A kit comprising a first vessel containing a 3′-blockednucleotide and a second vessel containing a reagent having the formulaR2-O—NH₂, R2-O—NHCH₃, or R2-O—CH₂N₃ wherein R2 has a molecular weight ofat least 24 g/mol.

Embodiment S97. The kit of embodiment S96, wherein the 3′-blockednucleotide comprises a blocking moiety bonded directly to the ribose 3′carbon of the nucleotide; and the blocking moiety is —ONH₂, —ONHCH₃, or—OCH₂CH₃.

Embodiment S98. The kit of embodiment S96, wherein the 3′-blockednucleotide comprises a blocking moiety bonded directly to the ribose 3′carbon of the nucleotide; and the blocking moiety is —ONH₂.

Embodiment S99. The kit of one of embodiments S96 to 598, wherein the3′-protected nucleotide comprises a protecting moiety directlycovalently bonded to the ribose 3′ carbon of the nucleotide; and theprotecting moiety is a 3′ oxime moiety.

Embodiment S100. The kit of embodiment S99, wherein the —O-oxime moietyhas the formula:

—O—N═C(R3)(R4); and

R3 and R4 are independently hydrogen, substituted or unsubstitutedalkyl, substituted or unsubstituted alkenyl, substituted orunsubstituted alkynyl, substituted or unsubstituted heteroalkyl,substituted or unsubstituted cycloalkyl, substituted or unsubstitutedcycloalkenyl, substituted or unsubstituted cycloalkynyl, substituted orunsubstituted aryl, substituted or unsubstituted heteroaryl, substitutedor unsubstituted heteroalicyclyl, substituted or unsubstituted aralkyl,substituted or unsubstituted heteroaralkyl, or substituted orunsubstituted (heteroalicyclyl)alkyl.

Embodiment S101. The kit of embodiment S99, wherein the —O-oxime moietyhas the formula:

—O—N═C(R3)(R4);

R3 is hydrogen; andR4 is substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted cycloalkenyl, substituted or unsubstitutedcycloalkynyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl, substituted or unsubstituted heteroalicyclyl,substituted or unsubstituted aralkyl, substituted or unsubstitutedheteroaralkyl, or substituted or unsubstituted (heteroalicyclyl)alkyl.

Embodiment S102. The kit of embodiment S99, wherein the —O-oxime moietyhas the formula:

—O—N═C(R3)(R4); and

R3 and R4 are independently substituted or unsubstituted alkyl,substituted or unsubstituted alkenyl, substituted or unsubstitutedalkynyl, substituted or unsubstituted heteroalkyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl,substituted or unsubstituted cycloalkynyl, substituted or unsubstitutedaryl, substituted or unsubstituted heteroaryl, substituted orunsubstituted heteroalicyclyl, substituted or unsubstituted aralkyl,substituted or unsubstituted heteroaralkyl, or substituted orunsubstituted (heteroalicyclyl)alkyl.

Embodiment S103. The kit of one of embodiments S96 to S102, wherein the3′-blocked nucleotide and the 3′-protected nucleotide comprise anadenine moiety or derivative thereof, guanine moiety or derivativethereof, cytosine moiety or derivative thereof, thymine moiety orderivative thereof, or uracil moiety or derivative thereof.

Embodiment S104. The kit of embodiment S103, wherein the adeninederivative moiety, guanine derivative moiety, cytosine derivativemoiety, thymine derivative moiety, and uracil derivative moiety comprisea detectable moiety.

Embodiment S105. The kit of one of embodiments S96 to S104, wherein the3′-blocked nucleotide and the 3′-protected nucleotide comprise amonophosphate moiety or derivative thereof, diphosphate moiety orderivative thereof, triphosphate moiety or derivative thereof, ormonovalent nucleic acid moiety or derivative thereof.

Embodiment S106. The kit of embodiment S105, wherein the 3′-blockednucleotide and the 3′-protected nucleotide comprise a monophosphatemoiety, diphosphate moiety, triphosphate moiety, or monovalent nucleicacid moiety.

Embodiment S107. The kit of embodiment S105, wherein the 3′-blockednucleotide and the 3′-protected nucleotide comprise a triphosphatemoiety.

Embodiment S108. The kit of embodiment S105, wherein the 3′-blockednucleotide and the 3′-protected nucleotide comprise a monovalent nucleicacid moiety.

Embodiment S109. The kit of one of embodiments S96 to S108, wherein the3′-blocked nucleotide and the 3′-protected nucleotide comprise a ribosemoiety.

Embodiment S110. The kit of one of embodiments S96 to S108, wherein the3′-blocked nucleotide and the 3′-protected nucleotide comprise a 2′deoxyribose moiety.

Embodiment S111. The kit of one of embodiments S96 to S110, wherein R2has a molecular weight of 1000 g/mol or less.

Embodiment S112. The kit of one of embodiments S96 to S111, wherein R2has a molecular weight of at least 36 g/mol.

Embodiment S113. The kit of one of embodiments S96 to S111, wherein R2has a molecular weight of at least 57 g/mol.

Embodiment S114. The kit of one of embodiments S96 to S111, wherein R2is substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted cycloalkyl, substituted or unsubstituted cycloalkenyl,substituted or unsubstituted cycloalkynyl, substituted or unsubstitutedaryl, substituted or unsubstituted heteroaryl, substituted orunsubstituted heteroalicyclyl, substituted or unsubstituted aralkyl,substituted or unsubstituted heteroaralkyl, or substituted orunsubstituted (heteroalicyclyl)alkyl.

Embodiment S115. The kit of one of embodiments S96 to S111, wherein R2is —C(R6)(R7)(R8), —C(O)(R6), —P(O)(R6)(R7), —C(R6)(═C(R7)(R8)),—Si(R6)(R7)(R8), —S O₂(R6), substituted or unsubstituted cycloalkyl,substituted or unsubstituted cycloalkenyl, substituted or unsubstitutedcycloalkynyl, substituted or unsubstituted heteroalicyclyl, substitutedor unsubstituted aryl, substituted or unsubstituted heteroaryl; and

R6, R7, and R8 are independently hydrogen,halogen, —CCl₃, —CBr₃, —CF₃, —CI₃, —CHCl₂, —CHBr₂, —CHF₂, —CHI₂, —CH₂Cl,—CH₂Br, —CH₂F, —CH₂I, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₃H,—SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂, —NHSO₂H,—NHC(O)H, —NHC(O)OH, —NHOH, —OCCl₃, —OCF₃, —OCBr₃—OCI₃, —OCHCl₂,—OCHBr₂, —OCHI₂, —OCHF₂, —OCH₂Cl, —OCH₂Br, —OCH₂I, —OCH₂F, —SF₅, —N₃,substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted cycloalkenyl, substituted or unsubstitutedcycloalkynyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl, substituted or unsubstituted heteroalicyclyl,substituted or unsubstituted aralkyl, substituted or unsubstitutedheteroaralkyl, or substituted or unsubstituted (heteroalicyclyl)alkyl.

Embodiment S116. The kit of embodiment S115, wherein R2 is—C(R6)(R7)(R8) and R6, R7, and R8 are not all hydrogen.

Embodiment S117. The kit of embodiment S115, wherein R2 is notunsubstituted methyl.

Embodiment S118. The kit of embodiment S115, wherein R2 is notunsubstituted ethyl.

Embodiment S119. The kit of embodiment S115, wherein R2 is notunsubstituted propyl.

Embodiment S120. The kit of one of embodiments S96 to S111, wherein R2is —C(R6)(R7)(R8), —C(O)(R6), —P(O)(R6)(R7), —C(R6)(═C(R7)(R8)),—Si(R6)(R7)(R8), —S O2(R6), unsubstituted 6 membered heteroalicyclyl,unsubstituted phenyl, substituted or unsubstituted heteroaryl; and

R6, R7, and R8 are independently hydrogen,halogen, —CCl₃, —CBr₃, —CF₃, —CI₃, —CHCl₂, —CHBr₂, —CHF₂, —CHI₂, —CH₂Cl,—CH₂Br, —CH₂F, —CH₂I, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₃H,—SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂, —NHSO₂H,—NHC(O)H, —NHC(O)OH, —NHOH, —OCCl₃, —OCF₃, —OCBr₃, —OCI₃, —OCHCl₂,—OCHBr₂, —OCHI₂, —OCHF₂, —OCH₂Cl, —OCH₂Br, —OCH₂I, —OCH₂F, —SF₅, —N₃,substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted cycloalkenyl, substituted or unsubstitutedcycloalkynyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl, substituted or unsubstituted heteroalicyclyl,substituted or unsubstituted aralkyl, substituted or unsubstitutedheteroaralkyl, or substituted or unsubstituted (heteroalicyclyl)alkyl.

Embodiment S121. The kit of embodiment S120, wherein R2 is—C(R6)(R7)(R8) and R6, R7, and R8 are not all hydrogen.

Embodiment S122. The kit of embodiment S120, wherein R2 is notunsubstituted methyl.

Embodiment S123. The kit of embodiment S120, wherein R2 is notunsubstituted ethyl.

Embodiment S124. The kit of embodiment S120, wherein R2 is notunsubstituted propyl.

Embodiment S125. The kit of one of embodiments S96 to S111, wherein thereagent has the formula:

Embodiment S126. The kit of one of embodiments S96 to S111, wherein thereagent has the formula:

Embodiment S127. The kit of one of embodiments S96 to S100, wherein the3′-protected nucleotide has the structure:

the 3′-blocked nucleotide has the structure:

B is a nucleobase;R1 is hydrogen, —OH, halogen, —OCH₃;Q is independently a nucleic acid moiety, triphosphate moiety,diphosphate moiety, or monophosphate moiety; andR3 and R4 are independently hydrogen, substituted or unsubstitutedalkyl, substituted or unsubstituted alkenyl, substituted orunsubstituted alkynyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted cycloalkenyl, substituted or unsubstitutedcycloalkynyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl, substituted or unsubstituted heteroalicyclyl,substituted or unsubstituted aralkyl, substituted or unsubstitutedheteroaralkyl, or substituted or unsubstituted (heteroalicyclyl)alkyl.

Embodiment S128. A kit comprising a first vessel containing a nucleotidecomprising a 3′-O-oxime moiety and a second vessel containing a reagentcomprising the structure R2-O—NH₂, wherein R2 is independently alkyl,alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl,heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl,(heteroalicyclyl)alkyl, or an optionally substituted variant thereof.

Embodiment S129. The kit of embodiment S128, wherein the nucleotidecomprises the structure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

Embodiment S130. The kit of one of embodiments S128 to S129, wherein thenucleobase comprises an exogenous label moiety.

Embodiment S131. The kit of one of embodiments S128 to S130, wherein theR2-O—NH₂ molecule is independently one of:

Embodiment T1. A method of adding a 3′-O—NH₂ moiety to a nucleotidehaving a 3′ protecting group, comprising contacting a nucleotide havinga 3′ protecting group to a reagent comprising the structure R2-O—NH₂,wherein R2 has a molecular weight of at least 24.

Embodiment T2. The method of embodiment T1, wherein the nucleotidehaving a 3′ protecting group comprises ribose.

Embodiment T3. The method of embodiment T1, wherein the nucleotidehaving a 3′ protecting group comprises 2′ deoxyribose.

Embodiment T4. The method of embodiment T2, wherein the nucleotidehaving a 3′ protecting group comprises phosphate.

Embodiment T5. The method of embodiment T4, wherein the nucleotidehaving a 3′ protecting group comprises triphosphate.

Embodiment T6. The method of embodiment T3, wherein the nucleotidehaving a 3′ protecting group comprises phosphate.

Embodiment T7. The method of embodiment T6, wherein the nucleotidehaving a 3′ protecting group comprises triphosphate.

Embodiment T8. The method of embodiment T1, wherein R2 has a molecularweight of at least 36.

Embodiment T9. The method of embodiment T1, wherein R2 comprises afluorine nucleus.

Embodiment T10. The method of embodiment T1, wherein R2 comprises atleast two carbon nuclei.

Embodiment T11. The method of embodiment T1, wherein R2 comprises acarbon-carbon double bond.

Embodiment T12. The method of embodiment T1, wherein R2 comprises atertiary carbon.

Embodiment T13. The method of embodiment T12, wherein R2 comprises atert-butyl moiety.

Embodiment T14. The method of embodiment T1, wherein R2 comprises acyclic moiety.

Embodiment T15. The method of embodiment T1, wherein R2 comprises asilicon nucleus.

Embodiment T16. The method of embodiment T1, wherein R2 comprises aphenyl ring.

Embodiment T17. The method of embodiment T1, wherein R2 comprises anitrogen nucleus.

Embodiment T18. The method of embodiment T1, wherein R2 comprises anoxygen nucleus.

Embodiment T19. The method of embodiment T1, wherein R2 comprises ahydroxylate moiety.

Embodiment T20. The method of embodiment T1, wherein the reagentcomprising the structure R2-O—NH₂ is selected from the group consistingof:

Embodiment T21. The method of embodiment T20, wherein the reagentcomprising the structure R2-O—NH₂ is

Embodiment T22. The method of embodiment T20, wherein the reagentcomprising the structure R2-O—NH₂ is

Embodiment T23. The method of embodiment T1, wherein the reagentcomprising the structure R2-O—NH₂ is selected from the group consistingof.

Embodiment T24. The method of any one of embodiments T8 to T23, whereinthe 3′ blocking group comprises 3′-O-Oxime.

Embodiment T25. The method of any one of embodiments T8 to T23, whereinthe 3′ blocking group comprises 3′-O-aldoxime.

Embodiment T26. The method of any one of embodiments T8 to T23, whereinthe 3′ blocking group comprises 3′-O-ketoxime.

Embodiment T27. The method of any one of embodiments T8 to T23, whereinthe nucleotide having a 3′ protecting group comprises the structure:

wherein the nucleotide that comprises the 3′-O—NH₂ moiety comprises thestructure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

Embodiment T28. The method of any one of embodiments T1 to T27, whereinthe method adds a 3′ ONH₂ in place of a 3′ protecting group to at least94% of a population of nucleotides having a 3′ protecting group in nomore than 3 hours.

Embodiment T29. The method of any one of embodiments T1 to T27, whereinthe method adds a 3′ ONH₂ in place of a 3′ protecting group to at least96% of a population of nucleotides having a 3′ protecting group in nomore than 3 hours.

Embodiment T30. The method of any one of embodiments T1 to T27, whereinthe method adds a 3′ ONH₂ in place of a 3′ protecting group to at least98% of a population of nucleotides having a 3′ protecting group in nomore than 3 hours.

Embodiment T31. The method of any one of embodiments T1 to T27, whereinthe method adds a 3′ ONH₂ in place of a 3′ protecting group to at least98% of a population of nucleotides having a 3′ protecting group in nomore than 2 hours.

Embodiment T32. The method of any one of embodiments T1 to T27, whereinthe method adds a 3′ ONH₂ in place of a 3′ protecting group to at least98% of a population of nucleotides having a 3′ protecting group in nomore than 1 hour.

Embodiment T33. The method of any one of embodiments T1 to T32, whereinthe nucleotide having a 3′ protecting group comprises cytosine, andwherein method degrades no more than 6% of cytosine bases from apopulation comprising a plurality of said nucleotide having a 3′protecting group comprising cytosine.

Embodiment T34. The method of any one of embodiments T1 to T32, whereinthe nucleotide having a 3′ protecting group comprises cytosine, andwherein method degrades no more than 5% of cytosine bases from apopulation comprising a plurality of said nucleotide having a 3′protecting group comprising cytosine.

Embodiment T35. The method of any one of embodiments T1 to T32, whereinthe nucleotide having a 3′ protecting group comprises cytosine, andwherein method degrades no more than 4% of cytosine bases from apopulation comprising a plurality of said nucleotide having a 3′protecting group comprising cytosine.

Embodiment T36. The method of any one of embodiments T1 to T32, whereinthe nucleotide having a 3′ protecting group comprises cytosine, andwherein method degrades no more than 3% of cytosine bases from apopulation comprising a plurality of said nucleotide having a 3′protecting group comprising cytosine.

Embodiment T37. The method of any one of embodiments T1 to T32, whereinthe nucleotide having a 3′ protecting group comprises cytosine, andwherein method degrades no more than 2% of cytosine bases from apopulation comprising a plurality of said nucleotide having a 3′protecting group comprising cytosine.

Embodiment T38. The method of any one of embodiments T1 to T32, whereinthe nucleotide having a 3′ protecting group comprises cytosine, andwherein method degrades no more than 1% of cytosine bases from apopulation comprising a plurality of said nucleotide having a 3′protecting group comprising cytosine.

Embodiment T39. A composition comprising a population of cytosinenucleotides wherein at least 94% of the population of cytosinenucleotides comprise a 3′-O—NH₂, wherein no more than 8% of thepopulation of cytosine nucleotides comprise a 3′ moiety other than—O—NH₂, and wherein no more than 6% of the population of cytosinenucleotides comprise a modified cytosine base.

Embodiment T40. The composition of embodiment T39, wherein at least 96%of the population of cytosine nucleotides comprise a 3′-O—NH₂.

Embodiment T41. The composition of embodiment T39, wherein at least 98%of the population of cytosine nucleotides comprise a 3′-O—NH₂.

Embodiment T42. The composition of embodiment T39, wherein at least 99%of the population of cytosine nucleotides comprise a 3′-O—NH₂.

Embodiment T43. The composition of embodiment T39, wherein no more than6% of the population of cytosine nucleotides comprise a 3′ moiety otherthan —O—NH₂.

Embodiment T44. The composition of embodiment T39, wherein no more than4% of the population of cytosine nucleotides comprise a 3′ moiety otherthan —O—NH₂.

Embodiment T45. The composition of embodiment T39, wherein no more than2% of the population of cytosine nucleotides comprise a 3′ moiety otherthan —O—NH₂.

Embodiment T46. The composition of embodiment T39, wherein no more than1% of the population of cytosine nucleotides comprise a 3′ moiety otherthan —O—NH₂.

Embodiment T47. The composition of embodiment T39, wherein no more than4% of the population of cytosine nucleotides comprise a modifiedcytosine base.

Embodiment T48. The composition of embodiment T39, wherein no more than2% of the population of cytosine nucleotides comprise a modifiedcytosine base.

Embodiment T49. The composition of embodiment T39, wherein no more than1% of the population of cytosine nucleotides comprise a modifiedcytosine base.

Embodiment T50. The composition of embodiment T39, wherein at least 98%of the population of cytosine nucleotides comprise a 3′-O—NH₂, whereinno more than 1% of the population of cytosine nucleotides comprise a 3′moiety other than —O—NH₂, and wherein no more than 1% of the populationof cytosine nucleotides comprise a modified cytosine base.

Embodiment T51. The composition of embodiment T39, wherein thecomposition is an aqueous solution.

Embodiment T52. The composition of embodiment T51, wherein the pH of thesolution is no less than 4 and no greater than 8.

Embodiment T53. The composition of embodiment T39, wherein thecomposition comprises a reagent comprising the structure R2-O—NH₂.

Embodiment T54. The composition of embodiment T53, wherein R2 comprisesa molecular weight of at least 24.

Embodiment T55. The composition of embodiment T53, wherein R2 comprisesa molecular weight of at least 36.

Embodiment T56. The composition of embodiment T53, wherein R2 comprisesa fluorine nucleus.

Embodiment T57. The composition of embodiment T53, wherein R2 comprisesat least two carbon nuclei.

Embodiment T58. The composition of embodiment T53, wherein R2 comprisesa carbon-carbon double bond.

Embodiment T59. The composition of embodiment T53, wherein R2 comprisesa tertiary carbon.

Embodiment T60. The composition of embodiment T59, wherein R2 comprisesa tert-butyl moiety.

Embodiment T61. The composition of embodiment T53, wherein R2 comprisesa cyclic moiety.

Embodiment T62. The composition of embodiment T53, wherein R2 comprisesa silicon nucleus.

Embodiment T63. The composition of embodiment T53, wherein R2 comprisesa phenyl ring.

Embodiment T64. The composition of embodiment T53, wherein R2 comprisesa nitrogen nucleus.

Embodiment T65. The composition of embodiment T53, wherein R2 comprisesan oxygen nucleus.

Embodiment T66. The composition of embodiment T53, wherein R2 comprisesa hydroxylated moiety.

Embodiment T67. The composition of embodiment T53, wherein the reagentcomprising the structure R2-O—NH₂ is selected from the group consistingof:

Embodiment T68. The composition of embodiment T53, wherein the reagentcomprising the structure R2-O—NH₂ is

Embodiment T69. The composition of embodiment T53, wherein the reagentcomprising the structure R2-O—NH₂ is

Embodiment T70. The composition of embodiment T53, wherein the reagentcomprising the structure R2-O—NH₂ is selected from the group consistingof:

Embodiment T71. The composition of any one of embodiments T39 to T70,wherein the 3′ moiety other than —O—NH₂ comprises a 3′ O-oxime.

Embodiment T72. The composition of any one of embodiments T39 to T70,wherein the 3′ moiety other than —O—NH₂ comprises a 3′ O-aldoxime.

Embodiment T73. The composition of any one of embodiments T39 to T70,wherein the 3′ moiety other than —O—NH₂ comprises a 3′ O-ketoxime.

Embodiment T74. The composition of embodiment T39, wherein thecomposition comprises a reagent comprising the structure R2-O—NHCH₃.

Embodiment T75. The composition of embodiment T39, wherein thecomposition comprises a reagent comprising the structure R2-O—CH₂N₃.

Embodiment T76. The composition of any one of embodiments T39 to T70,wherein at least some of the cytosine nucleotides having a 3′ moietyother than —O—NH₂ nucleotide comprise the structure:

wherein B is a cytosine nucleobase; R1 is independently halogen, OCH₃, Hor OH, Q is independently monophosphate, diphosphate, triphosphate, ornucleic acid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl,alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

Embodiment T77. A method of formulating a sequencing reagent, comprisingcontacting a composition comprising a 3′ protected nucleotide to areagent comprising a reversible terminator moiety to produce acomposition comprising a nucleotide comprising a reversible terminatormoiety, and formulating the composition comprising a nucleotidecomprising a reversible terminator moiety as a sequencing reagent,wherein formulating the composition comprising a reversible terminatormoiety does not comprise further purification of the compositioncomprising a reversible terminator moiety.

Embodiment T78. The method of embodiment T77, further comprisingapplying the sequencing reagent to a sequencing reagent to yield asequencing run of at least 100 bases having a quality score of at leastQ30.

Embodiment T79. The method of embodiment T77, wherein the reagentcomprising a reversible terminator moiety has a structure R2-O—NH₂.

Embodiment T80. The method of embodiment T79, wherein R2 comprises atleast two carbon nuclei, a fluorine nucleus, carbon-carbon double bond,tertiary carbon, tert-butyl moiety, cyclic moiety, silicon nucleus,phenyl ring, nitrogen nucleus, oxygen nucleus, or hydroxylate moiety.

Embodiment T81. The method of embodiment T80, wherein R2 comprises atleast two carbon nuclei, carbon-carbon double bond, tertiary carbon,tert-butyl moiety, cyclic moiety, or phenyl ring.

Embodiment T82. The method of embodiment T81, wherein R2 is —CH₂CH₃,—CH₂CHCH₂, or —C(CH₃)₃.

Embodiment T83. The method of embodiment T82, wherein R2 is —C(CH₃)₃.

Embodiment T84. The method of embodiment T79, wherein R2 has a molecularweight of at least 24.

Embodiment T85. The method of embodiment T84, wherein R2 has a molecularweight of at least 36.

Embodiment T86. The method of embodiment T84, wherein R2 has a molecularweight of at least 57.

Embodiment T87. The method of embodiment T84, wherein R2 has a molecularweight of at least 100.

Embodiment T88. The method of embodiment T84, wherein R2 has a molecularweight of at least 200.

Embodiment T89. The method of embodiment T84, wherein R2 has a molecularweight of at least 300.

Embodiment T90. The method of embodiment T84, wherein R2 has a molecularweight of at least 400.

Embodiment T91. The method of embodiment T84, wherein R2 has a molecularweight of at least 500.

Embodiment T92. The method of embodiment T84, wherein R2 has a molecularweight of at least 600.

Embodiment T93. The method of embodiment T84, wherein R2 has a molecularweight of at least 700.

Embodiment T94. The method of embodiment T84, wherein R2 has a molecularweight of at least 800.

Embodiment T95. The method of embodiment T84, wherein R2 has a molecularweight of at least 900.

Embodiment T96. The method of embodiment T79, wherein R2 comprises atleast two carbon nuclei.

Embodiment T97. The method of embodiment T79, wherein R2 comprises afluorine nucleus, silicon nucleus, nitrogen nucleus, oxygen nucleus, orhydroxylate moiety.

Embodiment T98. The method of embodiment T79, wherein the 3′ protectednucleotide comprises a 3′-O-oxime moiety.

Embodiment T99. The method of embodiment T98, wherein the oxime is analdoxime.

Embodiment T100. The method of embodiment T98, wherein the oxime is aketoxime.

Embodiment T101. The method of embodiment T79, wherein the compositioncomprising a nucleotide comprising a reversible terminator moietycomprises no more than 6% of the 3′ protected nucleotide relative to 3′protected nucleotide present initially.

Embodiment T102. The method of embodiment T101, wherein the compositioncomprising a nucleotide comprising a reversible terminator moietycomprises no more than 5% of the 3′ protected nucleotide relative to 3′protected nucleotide present initially.

Embodiment T103. The method of embodiment T101, wherein the compositioncomprising a nucleotide comprising a reversible terminator moietycomprises no more than 4% of the 3′ protected nucleotide relative to 3′protected nucleotide present initially.

Embodiment T104. The method of embodiment T101, wherein the compositioncomprising a nucleotide comprising a reversible terminator moietycomprises no more than 3% of the 3′ protected nucleotide relative to 3′protected nucleotide present initially.

Embodiment T105. The method of embodiment T101, wherein the compositioncomprising a nucleotide comprising a reversible terminator moietycomprises no more than 2% of the 3′ protected nucleotide relative to 3′protected nucleotide present initially.

Embodiment T106. The method of embodiment T101, wherein the compositioncomprising a nucleotide comprising a reversible terminator moietycomprises no more than 1% of the 3′ protected nucleotide relative to 3′protected nucleotide present initially.

Embodiment T107. The method of embodiment T79, wherein the compositioncomprising a nucleotide comprising a reversible terminator moietycomprises degraded or modified dC nucleobases at a concentration of nomore than 6% of total dC nucleobases in the composition comprising anucleotide comprising a reversible terminator moiety.

Embodiment T108. The method of embodiment T79, wherein the compositioncomprising a nucleotide comprising a reversible terminator moietycomprises degraded or modified dC nucleobases at a concentration of nomore than 5% of total dC nucleobases in the composition comprising anucleotide comprising a reversible terminator moiety.

Embodiment T109. The method of embodiment T79, wherein the compositioncomprising a nucleotide comprising a reversible terminator moietycomprises degraded or modified dC nucleobases at a concentration of nomore than 4% of total dC nucleobases in the composition comprising anucleotide comprising a reversible terminator moiety.

Embodiment T110. The method of embodiment T79, wherein the compositioncomprising a nucleotide comprising a reversible terminator moietycomprises degraded or modified dC nucleobases at a concentration of nomore than 3% of total dC nucleobases in the composition comprising anucleotide comprising a reversible terminator moiety.

Embodiment T111. The method of embodiment T79, wherein the compositioncomprising a nucleotide comprising a reversible terminator moietycomprises degraded or modified dC nucleobases at a concentration of nomore than 2% of total dC nucleobases in the composition comprising anucleotide comprising a reversible terminator moiety.

Embodiment T112. The method of embodiment T79, wherein the compositioncomprising a nucleotide comprising a reversible terminator moietycomprises degraded or modified dC nucleobases at a concentration of nomore than 1% of total dC nucleobases in the composition comprising anucleotide comprising a reversible terminator moiety.

Embodiment T113. A method for modifying a nucleotide, comprisingreacting a nucleotide comprising a 3′-O-oxime moiety with a reagentcomprising the structure R2-O—NH₂ to produce a nucleotide comprising a3′-O—NH₂ moiety, wherein R2 is independently alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

Embodiment T114. The method of embodiment T113, wherein the nucleotidethat comprises the 3′-O-oxime moiety comprises the structure:

wherein the nucleotide that comprises the 3′-O—NH₂ moiety comprises thestructure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

Embodiment T115. The method of embodiment T113, wherein the reactionoccurs in an aqueous solution.

Embodiment T116. The method of embodiment T115, wherein the nucleotideis attached to a solid support in contact with the aqueous solution.

Embodiment T117. The method of embodiment T115, wherein the reagent thatcomprises the structure R2-O—NH₂ is attached to a solid support incontact with the aqueous solution.

Embodiment T118. The method of any one of embodiments T113 to T117,wherein the nucleobase is a purine or pyrimidine.

Embodiment T119. The method of embodiment T118, wherein the nucleobaseis independently adenine, cytosine, guanine, thymine, or uracil.

Embodiment T120. The method of embodiment T118, wherein the nucleobaseis complementary to adenine, cytosine, guanine, thymine, or uracil.

Embodiment T121. The method of embodiment T118, wherein the nucleobaseis independently 5-methylcytosine, hypoxanthine, xanthine, inosine,isoguanine, isocytosine, or 7-deazaguanine.

Embodiment T122. The method of any one of embodiments T113 to T121,wherein the pH of the solution is no less than 4 and no greater than 8.

Embodiment T123. The method of any one of embodiments T113 to T122,wherein the nucleotide that is produced comprises a deoxynucleotide.

Embodiment T124. The method of embodiment T123, wherein the nucleotidethat is produced comprises:

wherein Base is the nucleobase, and wherein DNA is independently asingle stranded deoxyribonucleic acid or double strandeddeoxyribonucleic acid.

Embodiment T125. The method of any one of embodiments T113 to T124,wherein the reagent is independently one of.

Embodiment T126. A solution comprising a nucleotide comprising a3′-O-oxime moiety and a reagent comprising the structure R2-O—NH₂,wherein R2 is independently alkyl, alkenyl, alkynyl, cycloalkyl,cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl,heteroaralkyl, (heteroalicyclyl)alkyl, or an optionally substitutedvariant thereof.

Embodiment T127. The solution of embodiment T126, wherein the nucleotidecomprises the structure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

Embodiment T128. The solution of embodiment T127, wherein R1 is H.

Embodiment T129. The solution of embodiment T128, wherein Q isdeoxyribonucleic acid.

Embodiment T130. The solution of embodiment T127, wherein R1 is OH.

Embodiment T131. The solution of embodiment T130, wherein Q isribonucleic acid.

Embodiment T132. The solution of embodiment T126, wherein the solutionis an aqueous solution.

Embodiment T133. The solution of embodiment T132, wherein the nucleotideis attached to a solid support and wherein the solid support is incontact with the solution.

Embodiment T134 The solution of embodiment T132, wherein the reagentthat comprises the structure R2-O—NH₂ is attached to a solid support incontact with the aqueous solution.

Embodiment T135. The solution of any one of embodiments T126 to T134,wherein the nucleobase is a purine or pyrimidine.

Embodiment T136. The solution of embodiment T135, wherein the nucleobaseis independently adenine, cytosine, guanine, thymine, or uracil.

Embodiment T137. The solution of embodiment T135, wherein the nucleobaseis complementary to adenine, cytosine, guanine, thymine, or uracil.

Embodiment T138. The solution of embodiment T135, wherein the nucleobaseis independently 5-methylcytosine, hypoxanthine, xanthine, inosine,isoguanine, isocytosine, or 7-deazaguanine.

Embodiment T139. The solution of any one of embodiments T126 to T138,wherein the nucleobase comprises an exogenous label moiety.

Embodiment T140. The solution of any one of embodiments T126 to T139,wherein the pH of the solution is no less than 4 and no greater than 8.

Embodiment T141. The solution of any one of embodiments T126 to T140,wherein the R2-O—NH₂ molecule is independently one of:

Embodiment T142. A kit comprising a first vessel containing a nucleotidecomprising a 3′-O-oxime moiety and a second vessel containing a reagentcomprising the structure R2-O—NH₂, wherein R2 is independently alkyl,alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl,heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl,(heteroalicyclyl)alkyl, or an optionally substituted variant thereof.

Embodiment T143. The kit of embodiment T142, wherein the nucleotidecomprises the structure:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

Embodiment T144. The kit of embodiment T142, wherein the kit comprisesan RFID tag or bar code.

Embodiment T145. The kit of embodiment T143 or T144, wherein Q isindependently a single stranded deoxyribonucleic acid or double strandeddeoxyribonucleic acid.

Embodiment T146. The kit of embodiment T145, wherein the nucleotide isattached to a solid support.

Embodiment T147. The kit of embodiment T142, wherein the reagent thatcomprises the structure R2-O—NH₂ is attached to a solid support.

Embodiment T148. The kit of any one of embodiments T142 to T147, whereinthe nucleobase is a purine or pyrimidine.

Embodiment T149. The kit of embodiment T148, wherein the nucleobase isindependently adenine, cytosine, guanine, thymine, or uracil.

Embodiment T150. The kit of embodiment T148, wherein the nucleobase iscomplementary to adenine, cytosine, guanine, thymine, or uracil.

Embodiment T151. The kit of embodiment T148, wherein the nucleobase isindependently 5-methylcytosine, hypoxanthine, xanthine, inosine,isoguanine, isocytosine, or 7-deazaguanine.

Embodiment T152. The kit of any one of embodiments T142 to T151, whereinthe nucleobase comprises an exogenous label moiety.

Embodiment T153. The kit of any one of embodiments T142 to T152, whereinthe R2-O—NH₂ molecule is independently one of:

Additional Embodiments

Embodiment 1. A method of replacing a protecting group by a blockinggroup at a 3′ position of a nucleotide, comprising contacting thenucleotide and a reagent comprising the structure R2-block, wherein R2has a molecular weight of at least 24, wherein R2-block is watersoluble, and wherein block comprises a blocking group moiety.

Embodiment 2. The method of embodiment 1, wherein block comprises areversible terminator moiety.

Embodiment 3. The method of embodiment 2, wherein the reversibleterminator moiety does not preclude assembly of a nucleotide reversiblyterminated thereby into a ternary complex.

Embodiment 4. The method of any one of embodiments 1 to 3, whereinR2-block is selected from the group consisting of R2-O—NH₂, R2-O—NHCH₃,R2-O—NHCOCH₃, or R2-O—CH₂N₃.

Embodiment 5. The method of any one of embodiments 1 to 4, whereinR2-block is R2-O—CH₂N₃.

Embodiment 6. The method of any one of embodiments 1 to 4, whereinR2-block is R2-O—NH₂.

Embodiment 7. The method of any one of embodiments 1 to 4, wherein thenucleotide comprising a 3′ protecting group is:

wherein the nucleotide comprising a 3′ blocking group is:

wherein B is a nucleobase; R1 is independently halogen, OCH₃, H or OH, Qis independently monophosphate, diphosphate, triphosphate, or nucleicacid, and R3 and R4 are independently H, CH₃, alkyl, alkenyl, alkynyl,cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl,heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, or anoptionally substituted variant thereof.

Embodiment 8. The method of any one of embodiments 1 to 7, wherein theprotecting group comprises an —O-oxime.

Embodiment 9. The method of embodiment 8, wherein the —O-oxime moietyhas the formula: —O—N═C(R3)(R4); and R3 and R4 are independentlyhydrogen, substituted or unsubstituted alkyl, substituted orunsubstituted alkenyl, substituted or unsubstituted alkynyl, substitutedor unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted cycloalkenyl, substituted or unsubstitutedcycloalkynyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl, substituted or unsubstituted heteroalicyclyl,substituted or unsubstituted aralkyl, substituted or unsubstitutedheteroaralkyl, or substituted or unsubstituted (heteroalicyclyl)alkyl.

Embodiment 10. The method of embodiment 9, wherein R3 is Hydrogen.

Embodiment 11. The method of any one of embodiments 9 to 10, wherein R4is Hydrogen.

Embodiment 12. The method of any one of embodiments 1 to 11, wherein thenucleotide comprises a triphosphate moiety.

Embodiment 13. The method of any one of embodiments 1 to 4, wherein R2is —C(R6)(R7)(R8), —C(O)(R6), —P(O)(R6)(R7), —C(R6)(═C(R7)(R8)),—Si(R6)(R7)(R8), —S O₂(R6), substituted or unsubstituted cycloalkyl,substituted or unsubstituted cycloalkenyl, substituted or unsubstitutedcycloalkynyl, substituted or unsubstituted heteroalicyclyl, substitutedor unsubstituted aryl, substituted or unsubstituted heteroaryl; and

R6, R7, and R8 are independently hydrogen,halogen, —CCl₃, —CBr₃, —CF₃, —CI₃, —CHCl₂, —CHBr₂, —CHF₂, —CHI₂, —CH₂Cl,—CH₂Br, —CH₂F, —CH₂I, —CN, —OH, —NH₂, —COOH, —CONH₂, —NO₂, —SH, —SO₃H,—SO₄H, —SO₂NH₂, —NHNH₂, —ONH₂, —NHC(O)NHNH₂, —NHC(O)NH₂, —NHSO₂H,—NHC(O)H, —NHC(O)OH, —NHOH, —OCCl₃, —OCF₃, —OCBr₃, —OCI₃, —OCHCl₂,—OCHBr₂, —OCHI₂, —OCHF₂, —OCH₂Cl, —OCH₂Br, —OCH₂I, —OCH₂F, —SF₅, —N₃,substituted or unsubstituted alkyl, substituted or unsubstitutedalkenyl, substituted or unsubstituted alkynyl, substituted orunsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl,substituted or unsubstituted cycloalkenyl, substituted or unsubstitutedcycloalkynyl, substituted or unsubstituted aryl, substituted orunsubstituted heteroaryl, substituted or unsubstituted heteroalicyclyl,substituted or unsubstituted aralkyl, substituted or unsubstitutedheteroaralkyl, or substituted or unsubstituted (heteroalicyclyl)alkyl.

Embodiment 14. The method of embodiment 13, wherein R2 is —C(R6)(R7)(R8)and R6, R7, and R8 are not all hydrogen.

Embodiment 15. The method of embodiment 13, wherein R2 is notunsubstituted methyl.

Embodiment 16. The method of embodiment 13, wherein R2 is notunsubstituted ethyl.

Embodiment 17. The method of embodiment 13, wherein R2 is notunsubstituted propyl.

Embodiment 18. The method of embodiment 13, wherein R2-block has aformula selected from the group consisting of the following:

Embodiment 19. The method of embodiment 18, wherein R2-block has aformula selected from the group consisting of:

Embodiment 20. The method of embodiment 19, wherein R2-block has aformula

Embodiment 21. The method of embodiment 19, wherein R2-block has aformula

Embodiment 22. The method of embodiment 19, wherein R2-block has aformula

Embodiment 23. The method of embodiment 13, wherein R2 comprises ahydroxylated moiety.

Embodiment 24. The method of embodiment 13, wherein R2 comprises atleast two carbon nuclei, a fluorine nucleus, carbon-carbon double bond,tertiary carbon, tert-butyl moiety, cyclic moiety, silicon nucleus,phenyl ring, nitrogen nucleus, oxygen nucleus, or hydroxylate moiety.

Embodiment 25. The method of embodiment 13, wherein R2 has a molecularweight of no more than 280 g/mol.

Embodiment 26. The method of embodiment 13, wherein R2 has a molecularweight of no more than 100 g/mol.

Embodiment 27 The method of any one of embodiments 1 to 4, wherein themethod adds a blocking group in place of a 3′ protecting group to atleast 94% of a population of nucleotides having a 3′ protecting group inno more than 3 hours at 25° C.

Embodiment 28. The method of embodiment 27, wherein the method adds ablocking group in place of a 3′ protecting group to at least 98% of apopulation of nucleotides having a 3′ protecting group in no more than 3hours at 25° C.

Embodiment 29. The method of embodiment 28, wherein the method degradesno more than 6% of cytosine nucleobases in a population of nucleotideseach comprising a cytosine nucleobase.

Embodiment 30. The method of embodiment 29, wherein the method degradesno more than 1% of cytosine bases from the population of nucleotideshaving a cytosine nucleobase.

Embodiment 31. The method of any one of embodiments 1 to 19, wherein themethod adds a blocking group in place of a 3′ protecting group to atleast 94% of a population of nucleotides having a 3′ protecting group inno more than 3 hours at 25° C.

Embodiment 32. The method of embodiment 31, wherein the method adds ablocking group in place of a 3′ protecting group to at least 98% of apopulation of nucleotides having a 3′ protecting group in no more than 3hours at 25° C.

Embodiment 33. The method of embodiment 32, wherein the method degradesno more than 6% of cytosine nucleobases in a population of nucleotideseach comprising a cytosine nucleobase.

Embodiment 34. The method of embodiment 33, wherein the method degradesno more than 1% of cytosine nucleobases from the population ofnucleotides having a cytosine nucleobase.

EXAMPLES

Example 1. This example demonstrates the efficiency of nucleotidedeblocking using various alkoxyamine reagents and inertness of thedeblocking reagents to unwanted modification and degradation ofnucleotide structure. Each aminooxy deblocking reagent was formulated asa 3.2M solution in water, and the pH was adjusted to 5.25 with 10Msodium hydroxide. Each of these aminooxy solutions was then mixed 1:1with a 100 mM solution of dCTP oxime triphosphate and incubated at 25 Cfor 1 hr. At this time, the reaction was diluted 50-fold with 10%isopropyl methyl ketone in 50% isopropanol/water. Percent consumptionand degradation was analyzed by HPLC using a Phenomenex Gemini C18column (5 μm NX-X18 110 Å, LC Column 250×4.6 mm).

FIG. 1A shows a plot of percent nucleotide degradation vs. percentconsumption of 3′ oxime for dCTP when treated with various candidatereagents. The results indicate that when reacting dCTP-3′-oxime withreagents having structure R2-ONH₂, the species having the R2 moiety of—CH₃, —CH₂CH₃, —CH₂CHCH₂, or —C(CH₃)₃ produce a higher yield of 3′-ONH₂nucleotide compared to reaction with hydroxylamine. The candidatereagent having R2 moiety of —C(CH₃)₃ produced the highest yield of3′-ONH₂ nucleotide.

The results of FIG. 1A showed that the species having the R2 moiety of—CH₃, —CH₂CHCH₂, or —C(CH₃)₃ yielded substantially less unwanteddegradation of the nucleotide compared to treatment with hydroxylamine.Species having the R2 moiety of —CH₂CH₃ demonstrated a degradation levelthat was roughly comparable to treatment with hydroxylamine. The reagenthaving R2 moiety of —C(CH₃)₃ demonstrated the lowest level of unwantednucleotide degradation among the reagents tested in FIG. 1A.

Example 2. The composition of FIG. 1 produced through the use oftert-butyl-O—NH₂ was used to formulate a sequencing reagent withoutfurther purification. The sequencing reagent, which further comprised apolymerase was used in a sequencing run, and a read quality of at leastQ30 was observed for at least 100 bases of the read.

This example demonstrates that practice of the method herein producednucleotide compositions that are suitable to be formulated intosequencing reagents without further purification, such as sequencingreagents comprising a polymerase, surfactant, or other reagent suitablefor a sequencing reaction.

Throughout this application various publications, patents and/or patentapplications have been referenced. The disclosures of these documents intheir entireties are hereby incorporated by reference in thisapplication.

A number of embodiments have been described. Nevertheless, it will beunderstood that various modifications may be made. Accordingly, otherembodiments are within the scope of the following claims.

1.-30. (canceled)
 31. A method for modifying a nucleotide, comprisingreacting a nucleotide comprising a 3′-O-oxime moiety with a reagent toproduce a nucleotide comprising a 3′-O—NH₂ moiety, wherein thenucleotide that comprises the 3′-O-oxime moiety is:

wherein the nucleotide that comprises the 3′-O—NH₂ moiety is:

wherein B is a nucleobase; R1 is halogen, OCH₃, H or OH; Q ismonophosphate, diphosphate, or triphosphate; and R3 and R4 are H, CH₃,alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl,heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl, or(heteroalicyclyl)alkyl, wherein either R3 or R4, or both R3 and R4 arenot H; and; wherein the reagent is an alkoxyamine of formula R2-ONH₂,wherein R2 is independently alkyl, alkenyl, alkynyl, cycloalkyl,cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl,heteroaralkyl, (heteroalicyclyl)alkyl, or an optionally substitutedvariant thereof, wherein R2 has a molecular weight greater than 36g/mol.
 32. The method of claim 31, wherein R3 is CH₃.
 33. The method ofclaim 31, wherein R4 is CH₃.
 34. The method of claim 31, wherein Q istriphosphate.
 35. The method of claim 31, wherein the reagent is:


36. The method of claim 35, wherein the reagent is:


37. The method of claim 35, wherein the reagent is:


38. The method of claim 31, wherein R2 has a molecular weight greaterthan 57 g/mol.
 39. The method of claim 38, wherein R2 has a molecularweight greater than 100 g/mol.
 40. The method of claim 38, wherein R2has a molecular weight greater than 200 g/mol.
 41. The method of claim31, wherein R2 comprises a hydrocarbon ring.
 42. The method of claim 31,wherein R2 comprises a heterocyclic ring.
 43. The method of claim 31,wherein no more than 5% of the nucleotide is degraded.
 44. The method ofclaim 31, wherein no more than 3% of the nucleotide is degraded.
 45. Themethod of claim 31, wherein no more than 2% or no more than 1% of thenucleotide is degraded.
 46. The method of claim 31, wherein no more than3% of the nucleotide is degraded when the nucleotide comprises acytosine nucleobase.
 47. The method of claim 31, wherein the degradationof the nucleotide is less than half the degradation that would beobtained if R2 was a methyl group.
 48. The method of claim 31 or 43,wherein at least 95% of the nucleotide comprising a 3′-O-oxime moiety isconsumed.
 49. The method of claim 31, wherein at least 97% or at least98% of the nucleotide comprising a 3′-O-oxime moiety is consumed. 50.The method of claim 49, wherein the method adds a blocking group inplace of a 3′ protecting group to at least 98% of a population ofnucleotides having a 3′ protecting group in no more than 3 hours. 51.The method of claim 31, wherein R2-ONH₂ has a formula selected from thegroup consisting of the following: